In [1]:
rm(list=ls())
setwd("/hpc/group/pbenfeylab/CheWei/COPILOT_other_projects/Dusa_hg38_p13/")
In [2]:
suppressPackageStartupMessages({
    library(ggplot2)
    library(reshape2)
    #library(MAST)
    library(Matrix)
    library(Seurat)
    library(parallel)
    library(plyr)
    library(scales)
    library(ROCR)
    library(tidyverse)
    library(dplyr)
    library(patchwork)
    #library(Sushi)
    library(RColorBrewer)
    library(splines)
    #library(reticulate)
    #library(SeuratData)
    #library(SeuratWrappers)
    #library(SeuratDisk)
    #library(grid)
})
In [3]:
#citation("Sushi")
In [3]:
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: AlmaLinux 9.5 (Teal Serval)

Matrix products: default
BLAS/LAPACK: /hpc/group/pbenfeylab/ch416/miniconda3/envs/seu4/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3 patchwork_1.1.3    forcats_0.5.2      stringr_1.5.1     
 [5] dplyr_1.1.3        purrr_1.0.2        readr_2.1.3        tidyr_1.3.0       
 [9] tibble_3.2.1       tidyverse_1.3.2    ROCR_1.0-11        scales_1.2.1      
[13] plyr_1.8.9         SeuratObject_4.1.3 Seurat_4.1.1.9001  Matrix_1.5-4      
[17] reshape2_1.4.4     ggplot2_3.4.4     

loaded via a namespace (and not attached):
  [1] readxl_1.4.1           uuid_1.1-0             backports_1.4.1       
  [4] igraph_1.5.1           repr_1.1.4             lazyeval_0.2.2        
  [7] sp_2.1-1               RcppHNSW_0.5.0         listenv_0.9.0         
 [10] scattermore_1.2        digest_0.6.33          htmltools_0.5.7       
 [13] fansi_1.0.5            magrittr_2.0.3         tensor_1.5            
 [16] googlesheets4_1.0.1    cluster_2.1.4          tzdb_0.3.0            
 [19] globals_0.16.2         modelr_0.1.10          matrixStats_1.1.0     
 [22] timechange_0.1.1       spatstat.sparse_3.0-3  colorspace_2.1-0      
 [25] rvest_1.0.3            ggrepel_0.9.4          haven_2.5.1           
 [28] crayon_1.5.2           jsonlite_1.8.7         progressr_0.14.0      
 [31] spatstat.data_3.0-3    survival_3.4-0         zoo_1.8-12            
 [34] glue_1.6.2             polyclip_1.10-6        gtable_0.3.4          
 [37] gargle_1.2.1           leiden_0.4.3           future.apply_1.11.0   
 [40] abind_1.4-5            DBI_1.1.3              spatstat.random_3.2-1 
 [43] miniUI_0.1.1.1         Rcpp_1.0.11            viridisLite_0.4.2     
 [46] xtable_1.8-4           reticulate_1.34.0      htmlwidgets_1.6.2     
 [49] httr_1.4.7             ellipsis_0.3.2         ica_1.0-3             
 [52] pkgconfig_2.0.3        uwot_0.1.16            dbplyr_2.2.1          
 [55] deldir_1.0-9           utf8_1.2.4             tidyselect_1.2.0      
 [58] rlang_1.1.2            later_1.3.1            munsell_0.5.0         
 [61] cellranger_1.1.0       tools_4.2.2            cli_3.6.1             
 [64] generics_0.1.3         broom_1.0.2            ggridges_0.5.4        
 [67] evaluate_0.23          fastmap_1.1.1          goftest_1.2-3         
 [70] fs_1.6.3               fitdistrplus_1.1-11    RANN_2.6.1            
 [73] pbapply_1.7-2          future_1.33.0          nlme_3.1-162          
 [76] mime_0.12              xml2_1.3.3             compiler_4.2.2        
 [79] plotly_4.10.3          png_0.1-8              spatstat.utils_3.0-4  
 [82] reprex_2.0.2           stringi_1.8.1          RSpectra_0.16-1       
 [85] lattice_0.21-8         IRdisplay_1.1          vctrs_0.6.4           
 [88] pillar_1.9.0           lifecycle_1.0.4        spatstat.geom_3.2-7   
 [91] lmtest_0.9-40          RcppAnnoy_0.0.21       data.table_1.14.8     
 [94] cowplot_1.1.1          irlba_2.3.5.1          httpuv_1.6.12         
 [97] R6_2.5.1               promises_1.2.1         KernSmooth_2.23-20    
[100] gridExtra_2.3          parallelly_1.36.0      codetools_0.2-19      
[103] fastDummies_1.7.3      MASS_7.3-58.3          assertthat_0.2.1      
[106] withr_2.5.2            sctransform_0.4.1      hms_1.1.2             
[109] grid_4.2.2             IRkernel_1.3.1.9000    googledrive_2.0.0     
[112] Rtsne_0.16             pbdZMQ_0.3-8           spatstat.explore_3.2-5
[115] shiny_1.7.5.1          lubridate_1.9.0        base64enc_0.1-3       
In [4]:
# 202212 env
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /fast/home/c/chsu/anaconda3/envs/seu4/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.utf-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8    
 [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8   
 [7] LC_PAPER=en_US.utf-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] splines   parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3          Sushi_1.7.1                
 [3] biomaRt_2.54.0              zoo_1.8-11                 
 [5] patchwork_1.1.2             forcats_0.5.2              
 [7] stringr_1.4.1               dplyr_1.0.10               
 [9] purrr_0.3.5                 readr_2.1.3                
[11] tidyr_1.2.1                 tibble_3.1.8               
[13] tidyverse_1.3.2             ROCR_1.0-11                
[15] scales_1.2.1                plyr_1.8.8                 
[17] SeuratObject_4.1.3          Seurat_4.3.0               
[19] Matrix_1.5-3                MAST_1.24.0                
[21] SingleCellExperiment_1.20.0 SummarizedExperiment_1.28.0
[23] Biobase_2.58.0              GenomicRanges_1.50.0       
[25] GenomeInfoDb_1.34.3         IRanges_2.32.0             
[27] S4Vectors_0.36.0            BiocGenerics_0.44.0        
[29] MatrixGenerics_1.10.0       matrixStats_0.63.0         
[31] reshape2_1.4.4              ggplot2_3.4.0              

loaded via a namespace (and not attached):
  [1] readxl_1.4.1           uuid_1.1-0             backports_1.4.1       
  [4] BiocFileCache_2.6.0    igraph_1.3.5           repr_1.1.4            
  [7] lazyeval_0.2.2         sp_1.5-1               listenv_0.8.0         
 [10] scattermore_0.8        digest_0.6.30          htmltools_0.5.3       
 [13] fansi_1.0.3            memoise_2.0.1          magrittr_2.0.3        
 [16] tensor_1.5             googlesheets4_1.0.1    cluster_2.1.4         
 [19] tzdb_0.3.0             Biostrings_2.66.0      globals_0.16.2        
 [22] modelr_0.1.10          timechange_0.1.1       spatstat.sparse_3.0-0 
 [25] prettyunits_1.1.1      colorspace_2.0-3       rappdirs_0.3.3        
 [28] blob_1.2.3             rvest_1.0.3            ggrepel_0.9.2         
 [31] haven_2.5.1            crayon_1.5.2           RCurl_1.98-1.9        
 [34] jsonlite_1.8.3         progressr_0.11.0       spatstat.data_3.0-0   
 [37] survival_3.4-0         glue_1.6.2             polyclip_1.10-4       
 [40] gtable_0.3.1           gargle_1.2.1           zlibbioc_1.44.0       
 [43] XVector_0.38.0         leiden_0.4.3           DelayedArray_0.24.0   
 [46] future.apply_1.10.0    abind_1.4-5            DBI_1.1.3             
 [49] spatstat.random_3.0-1  miniUI_0.1.1.1         Rcpp_1.0.9            
 [52] progress_1.2.2         viridisLite_0.4.1      xtable_1.8-4          
 [55] reticulate_1.26        bit_4.0.5              htmlwidgets_1.5.4     
 [58] httr_1.4.4             ellipsis_0.3.2         ica_1.0-3             
 [61] XML_3.99-0.12          pkgconfig_2.0.3        uwot_0.1.14           
 [64] dbplyr_2.2.1           deldir_1.0-6           utf8_1.2.2            
 [67] AnnotationDbi_1.60.0   tidyselect_1.2.0       rlang_1.0.6           
 [70] later_1.2.0            cachem_1.0.6           munsell_0.5.0         
 [73] cellranger_1.1.0       tools_4.2.2            cli_3.4.1             
 [76] RSQLite_2.2.18         generics_0.1.3         broom_1.0.1           
 [79] ggridges_0.5.4         evaluate_0.18          fastmap_1.1.0         
 [82] goftest_1.2-3          bit64_4.0.5            fs_1.5.2              
 [85] fitdistrplus_1.1-8     RANN_2.6.1             KEGGREST_1.38.0       
 [88] pbapply_1.6-0          future_1.29.0          nlme_3.1-160          
 [91] mime_0.12              xml2_1.3.3             compiler_4.2.2        
 [94] filelock_1.0.2         curl_4.3.3             plotly_4.10.1         
 [97] png_0.1-7              spatstat.utils_3.0-1   reprex_2.0.2          
[100] stringi_1.7.8          lattice_0.20-45        IRdisplay_1.1         
[103] vctrs_0.5.1            pillar_1.8.1           lifecycle_1.0.3       
[106] spatstat.geom_3.0-3    lmtest_0.9-40          RcppAnnoy_0.0.20      
[109] data.table_1.14.6      cowplot_1.1.1          bitops_1.0-7          
[112] irlba_2.3.5.1          httpuv_1.6.6           R6_2.5.1              
[115] promises_1.2.0.1       KernSmooth_2.23-20     gridExtra_2.3         
[118] parallelly_1.32.1      codetools_0.2-18       MASS_7.3-58.1         
[121] assertthat_0.2.1       withr_2.5.0            sctransform_0.3.5     
[124] GenomeInfoDbData_1.2.9 hms_1.1.2              grid_4.2.2            
[127] IRkernel_1.3.1.9000    googledrive_2.0.0      Rtsne_0.16            
[130] pbdZMQ_0.3-8           spatstat.explore_3.0-5 lubridate_1.9.0       
[133] shiny_1.7.3            base64enc_0.1-3       
In [49]:
mt.genes <- as.character(read.table("../../Source_files/kallisto-bus/gtf_files/human_mt.txt", header=F)$V1)
id2name <- read.table("../../Source_files/kallisto-bus/gtf_files/hg38_p13_gene_id_name.txt", sep="\t", header=TRUE)
tt_id <- as.character(read.table("../../CW_data/Dusa/target_transcript_id.txt", header=F)$V1)
t_id <- unique(id2name$gene_id[sort(match(tt_id, id2name$transcript_id))])
grna_anno <- read.table("../../CW_data/Dusa/gRNA_list_complete.txt", sep="\t", header=FALSE)
grna_anno <- data.frame(grna_id=grna_anno$V1, type=grna_anno$V4)
grna_anno$order <- paste0("X",seq(1,1098,1))
control_idx <- grna_anno$order[which(grna_anno$type == "non-targctrl"| grna_anno$type == "NEG-CONTROL")]
target_idx <- grna_anno$order[which(grna_anno$type != "non-targctrl" & grna_anno$type != "NEG-CONTROL")]
pr_anno <- read.table("../../CW_data/Dusa/rhapsodygRNAs_promoter500.txt", sep="\t", header=FALSE)
colnames(pr_anno) <- c("chr", "start", "end", "strand", "name", "chr_prom", "start_prom", "end_prom", "prom_name", "overlap")
pr_anno$prom_name[which(pr_anno$prom_name == "AC195454.1")] <- "LINC02265"
pr_anno$prom_name[which(pr_anno$prom_name == "UCHL1-AS1")] <- "UCHL1.AS1"
pr_anno$prom_name[which(pr_anno$prom_name == "LVCAT1")] <- "LINC02475"
pr_anno$prom_name[which(pr_anno$prom_name == "RP11-663P9.2")] <- "NDUFB4P12"
pr_anno$prom_name[which(pr_anno$prom_name == "ZBTB12P1")] <- "ZBTB12BP"
In [12]:
genes.bed <- read.table("../../Source_files/kallisto-bus/gtf_files/Rhapsody_genes.bed")
colnames(genes.bed) <- c("chrom", "start", "stop","gene","score","strand","type")
#genes.bed$strand <- gsub("-","-1",gsub("\\+","+1",genes.bed$strand))
genes.bed$gene[which(genes.bed$gene == "AC195454.1")] <- "LINC02265"
genes.bed$gene[which(genes.bed$gene == "UCHL1-AS1")] <- "UCHL1.AS1"
genes.bed$gene[which(genes.bed$gene == "LVCAT1")] <- "LINC02475"
genes.bed$gene[which(genes.bed$gene == "RP11-663P9.2")] <- "NDUFB4P12"
genes.bed$gene[which(genes.bed$gene == "ZBTB12P1")] <- "ZBTB12BP"
genes.bed <- rbind(genes.bed,data.frame(chrom="chr4",start=41748293,stop=41824119,gene="AC105389.3",score=".",strand="+",type="gene"))
In [7]:
## Merge read counts from DBEC processed matrices
#UA9 <- read.table("../../Dusa/_1_UO_AH_902FW_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#UN <-  read.table("../../Dusa/_1_Undetermined_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#rownames(UA9) <- UA9$Cell_Index
#rownames(UN) <- UN$Cell_Index
#UA9 <- UA9[,-1]
#UN <- UN[,-1]
#shared <- UN[intersect(rownames(UN),rownames(UA9)),]
#uni <- UN[rownames(UN)[!rownames(UN) %in% intersect(rownames(UN),rownames(UA9))],]
#for (i in rownames(shared)){
#    UA9[i,] <- UA9[i,] + shared[i,]
#}
#UA9_BD <- rbind(UA9, uni)
#write.table(UA9_BD, file="../../Dusa/UA9_UN_BD.csv", quote=FALSE, sep=",")

#UA9 <- read.table("../../Dusa/UO_AH_934FW_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#UN <-  read.table("../../Dusa/Undetermined2_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#rownames(UA9) <- UA9$Cell_Index
#rownames(UN) <- UN$Cell_Index
#UA9 <- UA9[,-1]
#UN <- UN[,-1]
#shared <- UN[intersect(rownames(UN),rownames(UA9)),]
#uni <- UN[rownames(UN)[!rownames(UN) %in% intersect(rownames(UN),rownames(UA9))],]
#for (i in rownames(shared)){
#    UA9[i,] <- UA9[i,] + shared[i,]
#}
#UA9_BD <- rbind(UA9, uni)
#write.table(UA9_BD, file="../../Dusa/UA9_UN_BD_2.csv", quote=FALSE, sep=",")
In [7]:
## Raw counts from Rhapsody
R1 <- read.table("../../Dusa/UA9_UN_BD.csv", header=TRUE, sep=",")
R1 <- t(as.matrix(R1))
R2 <- read.table("../../Dusa/UA9_UN_BD_2.csv", header=TRUE, sep=",")
R2 <- t(as.matrix(R2))
In [8]:
#ngenes
nrow(R1)
nrow(R2)
#ncells
ncol(R1)
ncol(R2)
1176
1176
12597
19406
In [9]:
rownames(R1) <- gsub("_gencode","",rownames(R1))
rownames(R2) <- gsub("_gencode","",rownames(R2))
In [10]:
t_id <- rev(rownames(R1))[1:78] ## 78 targeted genes
t_idx <- sort(match(t_id,rownames(R1)));
g_idx <- seq(1,nrow(R1),1)[-t_idx]
tmtx1 <- R1[t_idx,] ## gene matrix
gmtx1 <- R1[g_idx,] ## gRNA matrix
r1 <- CreateSeuratObject(counts = R1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- subset(r1, features = t_id)
g1 <- subset(r1, features = rownames(gmtx1))
In [11]:
t_id <- rev(rownames(R2))[1:78]
t_idx <- sort(match(t_id,rownames(R2)));
g_idx <- seq(1,nrow(R2),1)[-t_idx]
tmtx2 <- R2[t_idx,]
gmtx2 <- R2[g_idx,]
r2 <- CreateSeuratObject(counts = R2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")
t2 <- subset(r2, features = t_id)
g2 <- subset(r2, features = rownames(gmtx2))
In [12]:
df <- data.frame(log10_gRNA_UMI_per_cell=log10(g1@meta.data$nCount_RNA),log10_gene_UMI_per_cell=log10(t1@meta.data$nCount_RNA))
d <- ggplot(df, aes(log10_gRNA_UMI_per_cell, log10_gene_UMI_per_cell))
d + geom_hex()+ geom_hline(yintercept=2, linetype="dashed", color = "red", size=2)+ geom_vline(xintercept=1.3, linetype="dashed", color = "red", size=2)

plot(density(log10(g1@meta.data$nCount_RNA)), main="log10_gRNA_UMI_per_cell")
abline(v = 1.3, col="red", lwd=3, lty=2)

plot(density(log10(t1@meta.data$nCount_RNA)), main="log10_gene_UMI_per_cell")
abline(v = 2, col="red", lwd=3, lty=2)

df <- data.frame(log10_gRNA_UMI_per_cell=log10(g2@meta.data$nCount_RNA),log10_gene_UMI_per_cell=log10(t2@meta.data$nCount_RNA))
d <- ggplot(df, aes(log10_gRNA_UMI_per_cell, log10_gene_UMI_per_cell))
d + geom_hex()+ geom_hline(yintercept=1.4, linetype="dashed", color = "red", size=2)+ geom_vline(xintercept=0.95, linetype="dashed", color = "red", size=2)

plot(density(log10(g2@meta.data$nCount_RNA)), main="log10_gRNA_UMI_per_cell")
abline(v = 0.95, col="red", lwd=3, lty=2)

plot(density(log10(t2@meta.data$nCount_RNA)), main="log10_gene_UMI_per_cell")
abline(v = 1.4, col="red", lwd=3, lty=2)
Warning message:
“Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.”
Warning message:
“Removed 1512 rows containing non-finite values (`stat_binhex()`).”
Warning message:
“Removed 3531 rows containing non-finite values (`stat_binhex()`).”
In [13]:
tmtx1 <- tmtx1[,which(log10(g1$nCount_RNA)>1.3 & log10(t1$nCount_RNA)>2)] ## gene matrix
gmtx1 <- gmtx1[,which(log10(g1$nCount_RNA)>1.3 & log10(t1$nCount_RNA)>2)] ## gRNA matrix
g1 <- CreateSeuratObject(counts = gmtx1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- CreateSeuratObject(counts = tmtx1[,colnames(g1)], min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

tmtx2 <- tmtx2[,which(log10(g2$nCount_RNA)>0.95 & log10(t2$nCount_RNA)>1.4)]
gmtx2 <- gmtx2[,which(log10(g2$nCount_RNA)>0.95 & log10(t2$nCount_RNA)>1.4)]
g2 <- CreateSeuratObject(counts = gmtx2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t2 <- CreateSeuratObject(counts = tmtx2[,colnames(g2)], min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
In [14]:
t1
g1
t2
g2
An object of class Seurat 
62 features across 6196 samples within 1 assay 
Active assay: RNA (62 features, 0 variable features)
An object of class Seurat 
1096 features across 6196 samples within 1 assay 
Active assay: RNA (1096 features, 0 variable features)
An object of class Seurat 
64 features across 10364 samples within 1 assay 
Active assay: RNA (64 features, 0 variable features)
An object of class Seurat 
1098 features across 10364 samples within 1 assay 
Active assay: RNA (1098 features, 0 variable features)
In [15]:
norm1 <- apply(as.matrix(g1@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(norm1[which(norm1>0)]))), main="log10_normalized_gRNA_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)
In [16]:
normt1 <- apply(as.matrix(t1@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(normt1[which(normt1>0)]))), main="log10_normalized_gene_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)
In [17]:
norm2 <- apply(as.matrix(g2@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(norm2[which(norm2>0)]))), main="log10_normalized_gRNA_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)
In [18]:
normt2 <- apply(as.matrix(t2@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(normt2[which(normt2>0)]))), main="log10_normalized_gene_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)
In [19]:
## Remove gRNA contribution (%) < 16: gRNA UMI counts/ total UMI counts per cell 
gmtx1 <- as.matrix(g1@assays$RNA@counts)
gmtx1[norm1<0.16]=0
g1 <- CreateSeuratObject(counts = gmtx1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- CreateSeuratObject(counts = tmtx1[,colnames(g1)], min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

gmtx2 <- as.matrix(g2@assays$RNA@counts)
gmtx2[norm2<0.16]=0
g2 <- CreateSeuratObject(counts = gmtx2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t2 <- CreateSeuratObject(counts = tmtx2[,colnames(g2)], min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
In [20]:
t1
g1
t2
g2
An object of class Seurat 
62 features across 6196 samples within 1 assay 
Active assay: RNA (62 features, 0 variable features)
An object of class Seurat 
1090 features across 6196 samples within 1 assay 
Active assay: RNA (1090 features, 0 variable features)
An object of class Seurat 
64 features across 10363 samples within 1 assay 
Active assay: RNA (64 features, 0 variable features)
An object of class Seurat 
1097 features across 10363 samples within 1 assay 
Active assay: RNA (1097 features, 0 variable features)
In [21]:
t1 <- NormalizeData(t1)
suppressWarnings(
t1 <- SCTransform(t1, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
g1 <- NormalizeData(g1)
suppressWarnings(
g1 <- SCTransform(g1, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
# Save Seurat object
save(t1,g1, file = "../../Dusa/Run1_filtered.rdata")
In [22]:
t2 <- NormalizeData(t2)
suppressWarnings(
t2 <- SCTransform(t2, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
g2 <- NormalizeData(g2)
suppressWarnings(
g2 <- SCTransform(g2, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
# Save Seurat object
save(t2,g2, file = "../../Dusa/Run2_filtered.rdata")
In [23]:
## Number of cells
ncol(t1)
ncol(g1)
ncol(t2)
ncol(g2)
6196
6196
10363
10363
In [24]:
load("../../Dusa/Run1_filtered.rdata")
load("../../Dusa/Run2_filtered.rdata")
In [25]:
t1
An object of class Seurat 
117 features across 6196 samples within 2 assays 
Active assay: SCT (55 features, 55 variable features)
 1 other assay present: RNA
In [26]:
t2
An object of class Seurat 
120 features across 10363 samples within 2 assays 
Active assay: SCT (56 features, 56 variable features)
 1 other assay present: RNA
In [27]:
## Normalized respectively
Comt <- merge(t1, y = t2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")
In [28]:
Comt <- SCTransform(Comt,vars.to.regress="orig.ident")
Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 59 by 16559

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 56 genes, 5000 cells

  |======================================================================| 100%
Second step: Get residuals using fitted parameters for 59 genes

  |======================================================================| 100%
Computing corrected count matrix for 59 genes

  |======================================================================| 100%
Calculating gene attributes

Wall clock passed: Time difference of 4.811563 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

In [29]:
Comt
An object of class Seurat 
125 features across 16559 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA
In [30]:
## SCTransform Var regress
df <- data.frame(RNA_count=colSums(Comt@assays$SCT@data), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized count)")+ylab("Cell count")+ggtitle("Normalized gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [31]:
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run1")]))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run2")]))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 
In [32]:
df <- data.frame(RNA_count=colSums(Comt@assays$RNA@counts), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw count (UMI)")+ylab("Cell count")+ggtitle("Gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [33]:
df <- data.frame(RNA_count=colSums(Comt@assays$RNA@data), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("LogNormalize")+ylab("Cell count")+ggtitle("Normalized gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [34]:
summary(colSums(t1@assays$RNA@counts))
summary(colSums(t2@assays$RNA@counts))
summary(colSums(t1@assays$RNA@data))
summary(colSums(t2@assays$RNA@data))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run1")]))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run2")]))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  101.0   525.8   802.0   859.5  1127.0  3223.0 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   26.0   144.0   212.0   240.7   305.0  1582.0 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  21.41   75.93   84.12   83.63   91.67  123.69 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  28.45   80.55   88.98   88.69   97.41  133.83 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 
In [35]:
## Normalize respectively
Comg <- merge(g1, y = g2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")
In [36]:
Comg <- SCTransform(Comg,vars.to.regress="orig.ident")
Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 1086 by 16559

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 650 genes, 5000 cells

  |======================================================================| 100%
There are 2 estimated thetas smaller than 1e-07 - will be set to 1e-07

Found 97 outliers - those will be ignored in fitting/regularization step


Second step: Get residuals using fitted parameters for 1086 genes

  |======================================================================| 100%
Computing corrected count matrix for 1086 genes

  |======================================================================| 100%
Calculating gene attributes

Wall clock passed: Time difference of 54.68452 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

In [37]:
Comg
An object of class Seurat 
2183 features across 16559 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA
In [38]:
## SCTransform var regress
df <- data.frame(RNA_count=colSums(Comg@assays$SCT@data), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized count)")+ylab("Cell count")+ggtitle("Normalized gRNA UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [39]:
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run1")]))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run2")]))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 
In [40]:
df <- data.frame(RNA_count=colSums(Comg@assays$RNA@counts), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw count (UMI)")+ylab("Cell count")+ggtitle("gRNA UMI count per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [41]:
df <- data.frame(RNA_count=colSums(Comg@assays$RNA@data), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("LogNormalize")+ylab("Cell count")+ggtitle("Normalized gRNA UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [42]:
summary(colSums(g1@assays$RNA@counts))
summary(colSums(g2@assays$RNA@counts))
summary(colSums(g1@assays$RNA@data))
summary(colSums(g2@assays$RNA@data))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run1")]))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run2")]))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   11.0   114.0   232.5   310.8   417.0  2958.0 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    4.0    38.0    75.0   108.8   142.0  1716.0 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.21    9.21    9.21   10.44    9.21   31.27 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.21    9.21    9.21   10.74    9.21   31.29 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 

gRNA calling¶

In [43]:
g1 <- subset(Comg, cells=colnames(Comg)[grep("^R1",colnames(Comg))])
g2 <- subset(Comg, cells=colnames(Comg)[grep("^R2",colnames(Comg))])
In [44]:
summary(colSums(g1@assays$SCT@data))
summary(colSums(g2@assays$SCT@data))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 
In [45]:
t1 <- subset(Comt, cells=colnames(Comt)[grep("^R1",colnames(Comt))])
t2 <- subset(Comt, cells=colnames(Comt)[grep("^R2",colnames(Comt))])
In [46]:
summary(colSums(t1@assays$SCT@data))
summary(colSums(t2@assays$SCT@data))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 
In [47]:
## Before and after normalization and gRNA thresholding 
# Raw counts
gr1 <- as.matrix(g1@assays$RNA@counts)
#threshold
gr1[gr1>0]=1
# filter out those don't have gRNA
#gr1 <- gr1[,-which(colSums(gr1)==0)]
#control cells
grc1 <- apply(gr1[sort(match(control_idx, rownames(gr1))),],2,function(x) any(x > 0)) & apply(gr1[sort(match(target_idx, rownames(gr1))),],2,function(x) all(x == 0))

gr2 <- as.matrix(g2@assays$RNA@counts)
#threshold
gr2[gr2>0]=1
# filter out those don't have gRNA
#gr2 <- gr2[,-which(colSums(gr2)==0)]
#control cells
grc2 <- apply(gr2[sort(match(control_idx, rownames(gr2))),],2,function(x) any(x > 0)) & apply(gr2[sort(match(target_idx, rownames(gr2))),],2,function(x) all(x == 0))
                                                                                              
# Raw counts with > 1 counts/gRNA threshold
grt1 <- as.matrix(g1@assays$RNA@counts)
#threshold
grt1[grt1<=1]=0                                                                                               
grt1[grt1>1]=1 
# filter out those don't have gRNA
#grt1 <- grt1[,-which(colSums(grt1)==0)]                                                                                              
#control cells
grtc1 <- apply(grt1[sort(match(control_idx, rownames(grt1))),],2,function(x) any(x > 0)) & apply(grt1[sort(match(target_idx, rownames(grt1))),],2,function(x) all(x == 0))

grt2 <- as.matrix(g2@assays$RNA@counts)
#threshold
grt2[grt2<=1]=0                                                                                               
grt2[grt2>1]=1
# filter out those don't have gRNA
#grt2 <- grt2[,-which(colSums(grt2)==0)]                                                                                                 
#control cells
grtc2 <- apply(grt2[sort(match(control_idx, rownames(grt2))),],2,function(x) any(x > 0)) & apply(grt2[sort(match(target_idx, rownames(grt2))),],2,function(x) all(x == 0))                                                                                       

# Normalized value (LogNormalize)
gnl1 <- as.matrix(g1@assays$RNA@data)
#threshold
gnl1[gnl1>0]=1
# filter out those don't have gRNA
#gnl1 <- gnl1[,-which(colSums(gnl1)==0)]                                                                                                  
#control cells
gnlc1 <- apply(gnl1[sort(match(control_idx, rownames(gnl1))),],2,function(x) any(x > 0)) & apply(gnl1[sort(match(target_idx, rownames(gnl1))),],2,function(x) all(x == 0))

gnl2 <- as.matrix(g2@assays$RNA@data)
#threshold
gnl2[gnl2>0]=1
# filter out those don't have gRNA
#gnl2 <- gnl2[,-which(colSums(gnl2)==0)]                                                                                                  
#control cells
gnlc2 <- apply(gnl2[sort(match(control_idx, rownames(gnl2))),],2,function(x) any(x > 0)) & apply(gnl2[sort(match(target_idx, rownames(gnl2))),],2,function(x) all(x == 0))   
                                                                                              
# Normalized value > 1 unit value/gRNA threshold
gnlt1 <- as.matrix(g1@assays$RNA@data)
#threshold
gnlt1[gnlt1<=1]=0                                                                                               
gnlt1[gnlt1>1]=1
# filter out those don't have gRNA
#gnlt1 <- gnlt1[,-which(colSums(gnlt1)==0)]                                                                                                 
#control cells
gnltc1 <- apply(gnlt1[sort(match(control_idx, rownames(gnlt1))),],2,function(x) any(x > 0)) & apply(gnlt1[sort(match(target_idx, rownames(gnlt1))),],2,function(x) all(x == 0))

gnlt2 <- as.matrix(g2@assays$RNA@data)
#threshold
gnlt2[gnlt2<=1]=0                                                                                               
gnlt2[gnlt2>1]=1
# filter out those don't have gRNA
#gnlt2 <- gnlt2[,-which(colSums(gnlt2)==0)]                                                                                                
#control cells
gnltc2 <- apply(gnlt2[sort(match(control_idx, rownames(gnlt2))),],2,function(x) any(x > 0)) & apply(gnlt2[sort(match(target_idx, rownames(gnlt2))),],2,function(x) all(x == 0)) 
                                                                                                 
# Normalized value (SCTrasform)
gn1 <- as.matrix(g1@assays$SCT@data)
#threshold
gn1[gn1>0]=1
# filter out those don't have gRNA
#gn1 <- gn1[,-which(colSums(gn1)==0)]                                                                                                
#control cells
gnc1 <- apply(gn1[sort(match(control_idx, rownames(gn1))),],2,function(x) any(x > 0)) & apply(gn1[sort(match(target_idx, rownames(gn1))),],2,function(x) all(x == 0))

gn2 <- as.matrix(g2@assays$SCT@data)
#threshold
gn2[gn2>0]=1
# filter out those don't have gRNA
#gn2 <- gn2[,-which(colSums(gn2)==0)]                                                                                          
#control cells
gnc2 <- apply(gn2[sort(match(control_idx, rownames(gn2))),],2,function(x) any(x > 0)) & apply(gn2[sort(match(target_idx, rownames(gn2))),],2,function(x) all(x == 0))   
                                                                                              
# Normalized value > 1 unit value/gRNA threshold
gnt1 <- as.matrix(g1@assays$SCT@data)
#threshold
gnt1[gnt1<=1]=0                                                                                               
gnt1[gnt1>1]=1
# filter out those don't have gRNA
#gnt1 <- gnt1[,-which(colSums(gnt1)==0)]                                                                                              
#control cells
gntc1 <- apply(gnt1[sort(match(control_idx, rownames(gnt1))),],2,function(x) any(x > 0)) & apply(gnt1[sort(match(target_idx, rownames(gnt1))),],2,function(x) all(x == 0))

gnt2 <- as.matrix(g2@assays$SCT@data)
#threshold
gnt2[gnt2<=1]=0                                                                                               
gnt2[gnt2>1]=1
# filter out those don't have gRNA
#gnt2 <- gnt2[,-which(colSums(gnt2)==0)]                                                                                                 
#control cells
gntc2 <- apply(gnt2[sort(match(control_idx, rownames(gnt2))),],2,function(x) any(x > 0)) & apply(gnt2[sort(match(target_idx, rownames(gnt2))),],2,function(x) all(x == 0))
In [48]:
dat <- data.frame(treatment=rep("Raw_1_Threshold_Run1", length(apply(gr1,2,sum))), gRNA_per_cell=apply(gr1,2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Raw_1_Threshold_Run2", length(apply(gr2,2,sum))), gRNA_per_cell=apply(gr2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Raw_2_Threshold_Run1", length(apply(grt1,2,sum))), gRNA_per_cell=apply(grt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Raw_2_Threshold_Run2", length(apply(grt2,2,sum))), gRNA_per_cell=apply(grt2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_1_Threshold_Run1", length(apply(gnl1,2,sum))), gRNA_per_cell=apply(gnl1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_1_Threshold_Run2", length(apply(gnl2,2,sum))), gRNA_per_cell=apply(gnl2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_2_Threshold_Run1", length(apply(gnlt1,2,sum))), gRNA_per_cell=apply(gnlt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_2_Threshold_Run2", length(apply(gnlt2,2,sum))), gRNA_per_cell=apply(gnlt2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_1_Threshold_Run1", length(apply(gn1,2,sum))), gRNA_per_cell=apply(gn1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_1_Threshold_Run2", length(apply(gn2,2,sum))), gRNA_per_cell=apply(gn2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_2_Threshold_Run1", length(apply(gnt1,2,sum))), gRNA_per_cell=apply(gnt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_2_Threshold_Run2", length(apply(gnt2,2,sum))), gRNA_per_cell=apply(gnt2,2,sum)))
In [49]:
dat <- within(dat, treatment <- factor(treatment, levels= c("Raw_1_Threshold_Run1","Raw_1_Threshold_Run2","Raw_2_Threshold_Run1","Raw_2_Threshold_Run2",
                                                            "LogNormalized_1_Threshold_Run1","LogNormalized_1_Threshold_Run2","LogNormalized_2_Threshold_Run1","LogNormalized_2_Threshold_Run2",
                                                            "SCTNormalized_1_Threshold_Run1","SCTNormalized_1_Threshold_Run2","SCTNormalized_2_Threshold_Run1","SCTNormalized_2_Threshold_Run2")))
In [50]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) +
geom_hline(yintercept=1, linetype="dashed", 
                color = "red", size=2)
In [51]:
pdf("gRNA_per_cell_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) +
geom_hline(yintercept=1, linetype="dashed", 
                color = "red", size=2)
dev.off()
png: 2
In [52]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) + coord_cartesian(ylim = c(0, 5))
In [53]:
pdf("gRNA_per_cell_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) + coord_cartesian(ylim = c(0, 5))
dev.off()
png: 2
In [54]:
cat("Raw_1_Threshold_Run1")
summary(dat[which(dat$treatment=="Raw_1_Threshold_Run1"),]$gRNA_per_cell)
cat("Raw_1_Threshold_Run2")
summary(dat[which(dat$treatment=="Raw_1_Threshold_Run2"),]$gRNA_per_cell)
cat("Raw_2_Threshold_Run1")
summary(dat[which(dat$treatment=="Raw_2_Threshold_Run1"),]$gRNA_per_cell)
cat("Raw_2_Threshold_Run2")
summary(dat[which(dat$treatment=="Raw_2_Threshold_Run2"),]$gRNA_per_cell)
cat("LogNormalized_1_Threshold_Run1")
summary(dat[which(dat$treatment=="LogNormalized_1_Threshold_Run1"),]$gRNA_per_cell)
cat("LogNormalized_1_Threshold_Run2")
summary(dat[which(dat$treatment=="LogNormalized_1_Threshold_Run2"),]$gRNA_per_cell)
cat("LogNormalized_2_Threshold_Run1")
summary(dat[which(dat$treatment=="LogNormalized_2_Threshold_Run1"),]$gRNA_per_cell)
cat("LogNormalized_2_Threshold_Run2")
summary(dat[which(dat$treatment=="LogNormalized_2_Threshold_Run2"),]$gRNA_per_cell)
cat("SCTNormalized_1_Threshold_Run1")
summary(dat[which(dat$treatment=="SCTNormalized_1_Threshold_Run1"),]$gRNA_per_cell)
cat("SCTNormalized_1_Threshold_Run2")
summary(dat[which(dat$treatment=="SCTNormalized_1_Threshold_Run2"),]$gRNA_per_cell)
cat("SCTNormalized_2_Threshold_Run1")
summary(dat[which(dat$treatment=="SCTNormalized_2_Threshold_Run1"),]$gRNA_per_cell)
cat("SCTNormalized_2_Threshold_Run2")
summary(dat[which(dat$treatment=="SCTNormalized_2_Threshold_Run2"),]$gRNA_per_cell)
Raw_1_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 
Raw_1_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 
Raw_2_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 
Raw_2_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 
LogNormalized_1_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 
LogNormalized_1_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 
LogNormalized_2_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 
LogNormalized_2_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 
SCTNormalized_1_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.158   1.000   4.000 
SCTNormalized_1_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.197   1.000   4.000 
SCTNormalized_2_Threshold_Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.158   1.000   4.000 
SCTNormalized_2_Threshold_Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.197   1.000   4.000 
In [55]:
apply(as.matrix(g1@assays$RNA@counts)[,colSums(grt1==1)==2],2,function(x){x[x>0]})
A matrix: 2 × 767 of type dbl
R1_669405R1_239628R1_150531R1_673925R1_174418R1_394891R1_879922R1_232726R1_645973R1_805522⋯R1_535059R1_258728R1_383082R1_806757R1_190872R1_97057R1_267545R1_312372R1_804603R1_593884
11561169642 957 996680891 8531021 735⋯18 913261723 623 618
971 890520128911118939061202 8971254⋯301916342622271229 5

Reproducibility¶

In [57]:
ep1 <- rowSums(t1@assays$RNA@data[intersect(rownames(t1),rownames(t2)),])/ncol(t1)
ep2 <- rowSums(t2@assays$RNA@data[intersect(rownames(t1),rownames(t2)),])/ncol(t2)
test <- data.frame(ep1=ep1,ep2=ep2)
mod = lm(ep1~ep2, data = test)
modsum = summary(mod)
ar2 = modsum$adj.r.squared
In [58]:
mod
Call:
lm(formula = ep1 ~ ep2, data = test)

Coefficients:
(Intercept)          ep2  
    0.08808      0.88425  
In [59]:
dat <- data.frame(ep1 = ep1, ep2 = ep2)
In [60]:
rsquared <- bquote(italic(R)^2 == .(format(ar2, digits = 3)))
pearsonr <- bquote(italic(r) == .(format(cor(ep1,ep2,method = "pearson"), digits = 3)))
options(repr.plot.width=8, repr.plot.height=8)
plot(ep1,ep2, xlab="Run1 pseudo-bulk expression profile ", ylab ="Run2 pseudo-bulk expression profile")
abline(lm(ep1 ~ ep2))
text(x = 200, y = 20, labels = rsquared)
text(x = 198, y = 15, labels = pearsonr)
In [61]:
ggplot(dat,aes(x=ep1,y=ep2))+ geom_point(size=3)+geom_abline(intercept = 0.08808, slope = 0.88425)+theme_classic()+ggtitle(bquote(.(rsquared)~.(pearsonr)))+xlab("Run1 pseudo-bulk expression profile")+ylab("Run2 pseudo-bulk expression profile")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [62]:
pdf("Reproducibility_202212.pdf",width=6,height=6)
ggplot(dat,aes(x=ep1,y=ep2))+ geom_point(size=3)+geom_abline(intercept = 0.09127, slope = 0.87948)+theme_classic()+ggtitle(bquote(.(rsquared)~.(pearsonr)))+xlab("Run1 pseudo-bulk expression profile")+ylab("Run2 pseudo-bulk expression profile")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2

Capture efficiency before gRNA thresholding and cell filtering¶

In [63]:
per.per.cell <- apply(gnt1,2,sum)
O <- table(per.per.cell)
loglik <- function(alpha, lambda, O) {
  krange <- as.integer(names(O))
  K <- max(krange)
sum(
  sapply(krange, function(k) O[as.character(k)] * log(sum( #k: number of guides observed
    sapply(max(c(k,1)):K, function(j) choose(j,k) * alpha ^ k * (1-alpha) ^ (j-k) * ( lambda ^ j / (factorial(j) * (exp(lambda) - 1))  )) #j: number of guides present
    )))
)
  
}
#Compiute log likelihood over parameter ranges
#moir <- seq(0,3,by=0.04)
moir <- 0.3 
alphar <- seq(0,1,by=0.001)
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gnt1.eff <- alphar[row]
In [64]:
#gnt1
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + 
scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + 
xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
Warning message:
“`qplot()` was deprecated in ggplot2 3.4.0.”
In [65]:
# gnt2
O2 <- table(apply(gnt2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gnt2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [66]:
# gn1
O2 <- table(apply(gn1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gn1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [67]:
# gn2
O2 <- table(apply(gn2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gn2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [68]:
# gr1
O2 <- table(apply(gr1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gr1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [69]:
# gr2
O2 <- table(apply(gr2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gr2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [70]:
# grt1
O2 <- table(apply(grt1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
grt1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())
In [71]:
# grt2
O2 <- table(apply(grt2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
grt2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

Capture efficiency after gRNA thresholding and cell filtering (raw vs SCTnormalized)¶

In [72]:
bardata <- data.frame(method = c("Raw_1_Threshold_Run1", "Raw_1_Threshold_Run2", "Raw_2_Threshold_Run1", "Raw_2_Threshold_Run2", "Normalized_1_Threshold_Run1", "Normalized_1_Threshold_Run2",  "Normalized_2_Threshold_Run1", "Normalized_2_Threshold_Run2"), eff = c(gr1.eff, gr2.eff, grt1.eff, grt2.eff, gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Raw_1_Threshold_Run1" = "#666666", "Raw_1_Threshold_Run2" = "#666666", "Raw_2_Threshold_Run1" = "#666666", "Raw_2_Threshold_Run2" = "#666666", "Normalized_1_Threshold_Run1" = "#666666", "Normalized_1_Threshold_Run2" = "#666666", "Normalized_2_Threshold_Run1" = "#666666", "Normalized_2_Threshold_Run2" = "#666666")) + 
theme_bw() + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black"), axis.text.x = element_text(angle=60, colour="black", hjust=1)) + xlab("") + ylab("gRNA capture efficiency") + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))
Warning message:
“The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.”
Warning message:
“The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in ggplot2 3.3.4.
ℹ Please use "none" instead.”
In [73]:
bardata <- data.frame(method = c("Before Filtering Run1", "Before Filtering Run2",  "After Filtering Run1", "After Filtering Run2"), eff = c(gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Before Filtering Run1" = "#666666", "Before Filtering Run2" = "#666666", "After Filtering Run1" = "#666666", "After Filtering Run2" = "#666666")) + 
theme_bw() + xlab("") + ylab("gRNA capture efficiency") + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black", size=16), axis.text.x = element_text( colour="black",size=16), axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))+ coord_flip()
In [74]:
pdf("gRNA_capture_efficiency_before_after_filtering_202212.pdf",width=6,height=6)
bardata <- data.frame(method = c("Before Filtering Run1", "Before Filtering Run2",  "After Filtering Run1", "After Filtering Run2"), eff = c(gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Before Filtering Run1" = "#666666", "Before Filtering Run2" = "#666666", "After Filtering Run1" = "#666666", "After Filtering Run2" = "#666666")) + 
theme_bw() + xlab("") + ylab("gRNA capture efficiency") + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black", size=16), axis.text.x = element_text( colour="black",size=16), axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))+ coord_flip()
dev.off()
png: 2
In [75]:
pdf("gRNA_capture_efficiency_202212.pdf",width=6,height=6)
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Raw_1_Threshold_Run1" = "#666666", "Raw_1_Threshold_Run2" = "#666666", "Raw_2_Threshold_Run1" = "#666666", "Raw_2_Threshold_Run2" = "#666666", "Normalized_1_Threshold_Run1" = "#666666", "Normalized_1_Threshold_Run2" = "#666666", "Normalized_2_Threshold_Run1" = "#666666", "Normalized_2_Threshold_Run2" = "#666666")) + 
theme_bw() + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black"), axis.text.x = element_text(angle=60, colour="black", hjust=1)) + xlab("") + ylab("gRNA capture efficiency") + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))
dev.off()
png: 2
In [76]:
cat("Raw_1_Threshold_Run1")
gr1.eff
cat("Raw_1_Threshold_Run2")
gr2.eff
cat("Raw_2_Threshold_Run1")
grt1.eff
cat("Raw_2_Threshold_Run2")
grt2.eff
cat("Normalized_1_Threshold_Run1")
gn1.eff
cat("Normalized_1_Threshold_Run2")
gn2.eff
cat("Normalized_2_Threshold_Run1")
gnt1.eff
cat("Normalized_2_Threshold_Run2")
gnt2.eff
Raw_1_Threshold_Run1
1
Raw_1_Threshold_Run2
1
Raw_2_Threshold_Run1
1
Raw_2_Threshold_Run2
1
Normalized_1_Threshold_Run1
0.998
Normalized_1_Threshold_Run2
0.998
Normalized_2_Threshold_Run1
0.998
Normalized_2_Threshold_Run2
0.998
In [77]:
# Nr cells
# Capture rate
length(colnames(t1)[which(apply(gr1,2,sum) != 0)])
length(colnames(t2)[which(apply(gr2,2,sum) != 0)])
length(colnames(t1)[which(apply(grt1,2,sum) != 0)])
length(colnames(t2)[which(apply(grt2,2,sum) != 0)])
length(colnames(t1)[which(apply(gn1,2,sum) != 0)])
length(colnames(t2)[which(apply(gn2,2,sum) != 0)])
length(colnames(t1)[which(apply(gnt1,2,sum) != 0)])
length(colnames(t2)[which(apply(gnt2,2,sum) != 0)])
6196
10363
6196
10363
6188
10347
6188
10347
In [78]:
# Capture rate
length(colnames(t1)[which(apply(gr1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gr2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(grt1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(grt2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(gn1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gn2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(gnt1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gnt2,2,sum) != 0)])/19406
0.491863142017941
0.534010099969082
0.491863142017941
0.534010099969082
0.491228070175439
0.533185612697104
0.491228070175439
0.533185612697104
In [79]:
# Number of control cells
sum(grc1)
sum(grc2)
sum(grtc1)
sum(grtc2)
sum(gnc1)
sum(gnc2)
sum(gntc1)
sum(gntc2)
206
370
206
370
206
370
206
370

gRNA threshold (bacth-corrected counts > 1)¶

In [56]:
gRNA_scheme1 <- gnt1[-sort(match(control_idx,rownames(gnt1))),]
gRNA_scheme1[gRNA_scheme1==1]="perturbed"
gRNA_scheme1[,gntc1] = "control"
gRNA_scheme1[gRNA_scheme1==0] = "perturbed_by_others"
t1@meta.data <- cbind(t1@meta.data, as.data.frame(t(gRNA_scheme1)))
gRNA_scheme2 <- gnt2[-sort(match(control_idx,rownames(gnt2))),]
gRNA_scheme2[gRNA_scheme2==1]="perturbed"
gRNA_scheme2[,gntc2] = "control"
gRNA_scheme2[gRNA_scheme2==0] = "perturbed_by_others"
t2@meta.data <- cbind(t2@meta.data, as.data.frame(t(gRNA_scheme2)))
In [57]:
br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(t1@meta.data))),]
#bin1 <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="control")>0)]="control"
#        dat[which(dat=='0')]="perturbed_by_others"
#    }
#    bin1 <- cbind(bin1,dat)
#} 
#colnames(bin1) <- names(table(br_anno$Bin))
reg1 <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="control")>0)]="control"
        dat[which(dat=='0')]="perturbed_by_others"
    }
    reg1 <- cbind(reg1,dat)
} 
colnames(reg1) <- names(table(br_anno$Region_name))
#t1@meta.data <- cbind(t1@meta.data,bin1)
t1@meta.data <- cbind(t1@meta.data,reg1)

br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(t2@meta.data))),]
#bin2 <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="control")>0)]="control"
#        dat[which(dat=='0')]="perturbed_by_others"
#    }
#    bin2 <- cbind(bin2,dat)
#} 
#colnames(bin2) <- names(table(br_anno$Bin))
reg2 <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="control")>0)]="control"
        dat[which(dat=='0')]="perturbed_by_others"
    }
    reg2 <- cbind(reg2,dat)
} 
colnames(reg2) <- names(table(br_anno$Region_name))
#t2@meta.data <- cbind(t2@meta.data,bin2)
t2@meta.data <- cbind(t2@meta.data,reg2)

Filter cells that don't contain any gRNA¶

In [58]:
t1 <- subset(t1, cells=colnames(t1)[which(apply(gnt1,2,sum) != 0)])
g1 <- subset(g1, cells=colnames(g1)[which(apply(gnt1,2,sum) != 0)])
t2 <- subset(t2, cells=colnames(t2)[which(apply(gnt2,2,sum) != 0)])
g2 <- subset(g2, cells=colnames(g2)[which(apply(gnt2,2,sum) != 0)])
save(t1,g1, file = "../../Dusa/Run1_filtered_2.rdata")
save(t2,g2, file = "../../Dusa/Run2_filtered_2.rdata")
In [59]:
load("../../Dusa/Run1_filtered_2.rdata")
load("../../Dusa/Run2_filtered_2.rdata")
In [60]:
t1
An object of class Seurat 
125 features across 6188 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA
In [61]:
g1
An object of class Seurat 
2183 features across 6188 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA
In [62]:
t2
An object of class Seurat 
125 features across 10347 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA
In [63]:
g2
An object of class Seurat 
2183 features across 10347 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA
In [64]:
summary(colSums(t1@assays$SCT@data))
summary(colSums(t2@assays$SCT@data))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.26   53.38 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.20   33.53   36.64   52.81 
In [65]:
summary(colSums(g1@assays$SCT@data))
summary(colSums(g2@assays$SCT@data))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.996   4.787   5.215   5.709   5.666  20.472 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.303   4.111   4.564   5.078   5.088  20.044 
In [66]:
Comt <- merge(t1, y = t2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")
In [67]:
Comt <- SCTransform(Comt, vars.to.regress = "orig.ident")
Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 59 by 16535

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 56 genes, 5000 cells

  |======================================================================| 100%
Second step: Get residuals using fitted parameters for 59 genes

  |======================================================================| 100%
Computing corrected count matrix for 59 genes

  |======================================================================| 100%
Calculating gene attributes

Wall clock passed: Time difference of 5.218403 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

In [68]:
Comt
An object of class Seurat 
125 features across 16535 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA
In [69]:
Comt@meta.data[is.na(Comt@meta.data)] <- "perturbed_by_others"
In [70]:
saveRDS(Comt, file = "./Rhapsody_BC.rds")
In [4]:
rc.integrated <- readRDS("./Rhapsody_BC.rds")
In [72]:
df <- data.frame(RNA_count=colSums(rc.integrated@assays$RNA@counts), Run=rc.integrated$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw counts (UMI)")+ylab("Cell count")+ggtitle("Gene UMI/cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))
In [73]:
df <- data.frame(RNA_count=colSums(rc.integrated@assays$SCT@data), Run=rc.integrated$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized counts)")+ylab("Cell count")+ggtitle("Batch-corrected normalized gene UMI/cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

Two runs vs integration¶

In [74]:
gint <- column_to_rownames(full_join(rownames_to_column(as.data.frame(g1@assays$SCT@data),var = "rownames"), rownames_to_column(as.data.frame(g2@assays$SCT@data),var="rownames"), by="rownames"), var = "rownames")
gint[is.na(gint)] <- 0
In [75]:
dat <- data.frame(treatment=rep("Run1", length(apply(g1@assays$SCT@data>1,1,sum))), nrcell_per_gRNA=apply(g1@assays$SCT@data>1,1,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(g2@assays$SCT@data>1,1,sum))), nrcell_per_gRNA=apply(g2@assays$SCT@data>1,1,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(gint>1,1,sum))), nrcell_per_gRNA=apply(gint>1,1,sum)))
In [76]:
dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))
In [77]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [78]:
pdf("nrcell_per_gRNA_2counts_1_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+ 
  theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [79]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 90))
In [80]:
pdf("nrcell_per_gRNA_2counts_2_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 90))
dev.off()
png: 2
In [81]:
## gRNA summary
cat("Run1")
summary(apply(g1@assays$SCT@data>1,1,sum))
cat("Run2")
summary(apply(g2@assays$SCT@data>1,1,sum))
cat("Integrated")
summary(apply(gint>1,1,sum))
Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.000   6.000   6.608   9.000  22.000 
Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   2.00    8.00   11.00   11.43   14.00   38.00 
Integrated
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   5.00   13.00   17.00   18.03   22.00   58.00 
In [82]:
## Region summary
rint <- column_to_rownames(full_join(rownames_to_column(as.data.frame(t(reg1)),var = "rownames"), rownames_to_column(as.data.frame(t(reg2)),var="rownames"), by="rownames"), var = "rownames")
rint[is.na(rint)] <- 0
In [83]:
dat <- data.frame(treatment=rep("Run1", length(apply(reg1=="perturbed",2,sum))), nrcell_per_region=apply(reg1=="perturbed",2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(reg2=="perturbed",2,sum))), nrcell_per_region=apply(reg2=="perturbed",2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(rint=="perturbed",1,sum))), nrcell_per_region=apply(rint=="perturbed",1,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))
In [84]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_region)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))
In [85]:
pdf("nrcell_per_region_2counts_1_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_region)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))
dev.off()
png: 2
In [86]:
dat <- data.frame(treatment=rep("gRNA", length(apply(gint>1,1,sum))), nrcell=apply(gint>1,1,sum))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(apply(bint=="perturbed",1,sum))), nrcell=apply(bint=="perturbed",1,sum)))
dat <- rbind(dat, data.frame(treatment=rep("region", length(apply(rint=="perturbed",1,sum))), nrcell=apply(rint=="perturbed",1,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","bin","region")))
In [87]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [89]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) +
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [90]:
dat %>% filter(treatment=='gRNA') %>% summary()
  treatment        nrcell     
 gRNA  :1086   Min.   : 5.00  
 bin   :   0   1st Qu.:13.00  
 region:   0   Median :17.00  
               Mean   :18.03  
               3rd Qu.:22.00  
               Max.   :58.00  
In [91]:
dat %>% filter(treatment=='region') %>% summary()
  treatment       nrcell      
 gRNA  :  0   Min.   :  9.00  
 bin   :  0   1st Qu.: 42.25  
 region:222   Median : 68.00  
              Mean   : 81.39  
              3rd Qu.: 96.25  
              Max.   :597.00  
In [88]:
pdf("nrcell_per_gRNA_region_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/bin/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [92]:
cat("Run1")
summary(apply(reg1=="perturbed",2,sum))
cat("Run2")
summary(apply(reg2=="perturbed",2,sum))
cat("Integrated")
summary(apply(rint=="perturbed",1,sum))
Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00   16.00   24.00   30.01   36.00  236.00 
Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   6.00   25.25   43.00   51.38   60.00  374.00 
Integrated
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.00   42.25   68.00   81.39   96.25  597.00 
In [93]:
dat <- data.frame(treatment=rep("Run1", length(apply(g1@assays$SCT@data>1,2,sum))), gRNA_per_cell=apply(g1@assays$SCT@data>1,2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(g2@assays$SCT@data>1,2,sum))), gRNA_per_cell=apply(g2@assays$SCT@data>1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(gint>1,2,sum))), gRNA_per_cell=apply(gint>1,2,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))
In [94]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [95]:
pdf("gRNA_per_cell_2counts_3_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [96]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 5))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [97]:
pdf("gRNA_per_cell_2counts_4_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 5))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [98]:
cat("Run1")
summary(apply(g1@assays$SCT@data>1,2,sum))
cat("Run2")
summary(apply(g2@assays$SCT@data>1,2,sum))
cat("Integrated")
summary(apply(gint>1,2,sum))
Run1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 
Run2
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.199   1.000   4.000 
Integrated
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.184   1.000   4.000 

Prepare for DE¶

In [99]:
#For each cell, how many of the genes were detected on average? A: 17
mean(apply(rc.integrated@assays$SCT@data,2,function(x){sum(x>0)}))
17.0035681886907
In [100]:
rc.integrated@meta.data <- rc.integrated@meta.data[,-grep("^PHOX2B|^Region",colnames(rc.integrated@meta.data))]
In [101]:
br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(rc.integrated@meta.data))),]
# Set all "perturbed_by_others" to "control" 
for (i in grep("^X",colnames(rc.integrated@meta.data))){
    rc.integrated@meta.data[,i] <- gsub("perturbed_by_others", "control", rc.integrated@meta.data[,i], ignore.case = FALSE, perl = FALSE,fixed = T, useBytes = FALSE)
}
# Set "control"s within same Region or +/- 400 kb distance region to "perturbed_by_others" 
for (i in 1:length(grep("^X",colnames(rc.integrated@meta.data)))){
    idx <- colnames(rc.integrated@meta.data[,grep("^X",colnames(rc.integrated@meta.data))][i])
    tidx <- which(br_anno$Rhapsody_name==colnames(rc.integrated@meta.data[,grep("^X",colnames(rc.integrated@meta.data))][i]))
    hidx <- br_anno$Rhapsody_name[which(br_anno$guide_start > (br_anno$guide_start[tidx]-400000) & br_anno$guide_start < (br_anno$guide_end[tidx]+400000) & br_anno$guide_end > (br_anno$guide_start[tidx]-400000) & br_anno$guide_end < (br_anno$guide_end[tidx]+400000))]
    kidx <- br_anno$Rhapsody_name[which(br_anno$Region_name==br_anno$Region_name[tidx])]
    ridx <- unique(hidx, kidx)
    
    if (length(ridx)>2){
        rc.integrated@meta.data[which(apply(rc.integrated@meta.data[,ridx[which(ridx != idx)]],1, function(x)sum(x=="perturbed"))>=1),idx]="perturbed_by_others"
    } else if (length(ridx)>1) {
        rc.integrated@meta.data[which(rc.integrated@meta.data[,ridx[which(ridx != idx)]]=="perturbed"),idx]="perturbed_by_others"
    }
}
In [102]:
#bin <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed_by_others")>=1 & dat!="perturbed")]="perturbed_by_others"
#        dat[which(dat=='0')]="control"
#    }
#    bin <- cbind(bin,dat)
#} 
#colnames(bin) <- names(table(br_anno$Bin))
reg <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed_by_others")>=1 & dat!="perturbed")]="perturbed_by_others"
        dat[which(dat=='0')]="control"
    }
    reg <- cbind(reg,dat)
} 
colnames(reg) <- names(table(br_anno$Region_name))

#rc.integrated@meta.data <- cbind(rc.integrated@meta.data,bin)
rc.integrated@meta.data <- cbind(rc.integrated@meta.data,reg)
In [103]:
TAP.nods <- as.matrix(rc.integrated@assays$SCT@data)
ngenes <- apply(TAP.nods > 0 , 2, sum)
In [104]:
hist(ngenes)
In [105]:
save(rc.integrated, ngenes, file = "../../Dusa/Rhapsody_MAST_input.rdata")
In [106]:
load(file = "../../Dusa/Rhapsody_MAST_input.rdata")

Plot gene expression level (SCT)¶

In [131]:
gene_name <- "PHOX2B"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])                                  
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
#+coord_cartesian(ylim = c(0, 60))
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 988327, p-value = 1.146e-09
alternative hypothesis: true location shift is not equal to 0
In [132]:
pdf("PHOX2B_expr_sct_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot()+theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()
png: 2
In [133]:
gene_name <- "SHISA3"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
                                 # + coord_cartesian(ylim = c(0, 25))
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 462772, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
In [134]:
pdf("SHISA3_expr_sct_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()
png: 2
In [135]:
gene_name <- "BEND4"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
                                  #+ coord_cartesian(ylim = c(0, 10))
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 376932, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
In [136]:
pdf("BEND4_expr_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()
png: 2

Differential Expression Analysis¶

In [137]:
TAP_DE <- c()

Run Suerat Test (gRNA)¶

In [138]:
gRNA_scheme <- t(as.matrix(rc.integrated@meta.data[,grep("^X", colnames(rc.integrated@meta.data))]))
In [139]:
table(gRNA_scheme[1,])
            control           perturbed perturbed_by_others 
              13350                  22                3163 
In [140]:
apply(gRNA_scheme,1,table)
A matrix: 3 × 1034 of type int
X1X10X100X1000X1001X1002X1003X1004X1005X1006⋯X993X994X995X996X997X998X999X1030X248X585
control13350129151144411137113461138511399972194378330⋯12664119181172211590115901159011246976566848041
perturbed 22 7 16 10 9 6 24 22 13 11⋯ 20 12 22 17 14 11 23 5 6 8
perturbed_by_others 3163 3613 5075 5388 5180 5144 5112679270858194⋯ 3851 4605 4791 4928 4931 4934 5266676598458486

MAST cov¶

In [141]:
de_MAST <- function(pert_object) {
  
  # add some row- and colData expected by MAST (not used in DE tests)
  rowData(pert_object) <- cbind(rowData(pert_object), primerid = rownames(pert_object))
  colData(pert_object) <- cbind(colData(pert_object), wellKey = colnames(pert_object))

  # coerce pert_object to SingleCellAssay, since MAST requires that as input
  sca <- SceToSingleCellAssay(pert_object)
  
  # prepare colData for model fitting
  colnames(colData(sca))[1] <- "pert"  # make sure 1st column is called pert for coeff testing
  pert <- as.factor(colData(sca)$pert)
  levels(pert) <- c(0, 1)
  colData(sca)$pert <- pert

  # fit hurdle model
  vars <- colnames(colData(sca))
  vars_to_test <- vars[vars != "wellKey"]
  model <- paste0("~", paste(vars_to_test, collapse = "+"))
  zlm_fit <- zlm(as.formula(model), sca)
  # get logFC change for the perturbation coefficient
  summary_zlm_fit <- summary(zlm_fit, logFC = TRUE)
  summary_dt <- summary_zlm_fit$datatable
  logFC <- summary_dt[contrast == "pert1" & component == "logFC", .(primerid, coef, ci.hi, ci.lo)]

  # perform likelihood ratio test for the perturbation coefficient
  lrt <- as.data.frame(lrTest(zlm_fit, CoefficientHypothesis("pert1")))
  lrt_output <- data.frame(primerid = rownames(lrt), pvalue = lrt[, "hurdle.Pr(>Chisq)"],
                           row.names = rownames(lrt), stringsAsFactors = FALSE)
 
  # assemble and return output
  output <- merge(as.data.frame(logFC), lrt_output, by = "primerid")
  colnames(output) <- c("gene", "logFC", "ci_high", "ci_low", "pvalue")
  output[order(output$pvalue), ]
  
}
In [142]:
## Use SCT assay data slot
runSeuratTest <- function(g = "X1", object=rc.integrated, covariate=ngenes) { 
  
  Idents(object) <- g
  object$covariate <- covariate
  a <- colnames(object)[Idents(object) == "perturbed"]
  b <- colnames(object)[Idents(object) == "control"]

  use.a <- a
  use.b <- b
  testobject <- subset(object, cells = c(use.a, use.b))
 
  a.obj <- subset(object, cells = use.a)
  b.obj <- subset(object, cells = use.b)

  sce <- SingleCellExperiment(list(counts = GetAssayData(testobject, assay = "SCT", slot = "data"), logcounts = GetAssayData(testobject, assay = "SCT", slot = "data")) , colData = data.frame(row.names = colnames(testobject), ident = Idents(testobject), cov = testobject$covariate))
 
  MAST.result <- de_MAST(sce)

  m <- data.frame(row.names =MAST.result$gene, p_val = MAST.result$pvalue, avg_logFC = MAST.result$logFC, pct.1="NA", pct.2="NA", p_val_adj = p.adjust( MAST.result$pvalue, method = "fdr"))
    
  m$gene <- rownames(m) 
  m$ident <- g
  m$method <- "MAST.cov"
  m$ncells <- length(a)
  m
}
In [ ]:
output <- lapply(rownames(gRNA_scheme), runSeuratTest, object = rc.integrated, covariate = ngenes)
output <- do.call(rbind, output)
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Done!

Combining coefficients and standard errors

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Refitting on reduced model...


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Assuming data assay in position 2, with name logcounts is log-transformed.


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Combining coefficients and standard errors

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 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures


 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

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 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

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 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

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 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

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 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

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 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

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 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

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 Completed [=================================>----------]  78% with 0 failures

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 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

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 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

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 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

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 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

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 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

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 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures
 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [======>-------------------------------------]  15% with 0 failures

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 Completed [============>-------------------------------]  29% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

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 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

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 Completed [================>---------------------------]  39% with 0 failures

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 Completed [========================================>---]  93% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

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 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

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 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

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 Completed [=======================>--------------------]  54% with 0 failures

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 Completed [===================================>--------]  81% with 0 failures

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 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

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 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

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 Completed [=================================>----------]  78% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

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 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

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 Completed [======================>---------------------]  53% with 0 failures

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 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures
 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

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Combining coefficients and standard errors

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Combining coefficients and standard errors

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In [ ]:
TAP_DE <- rbind(TAP_DE, output)

Run Suerat Test (region)¶

In [ ]:
gRNA_scheme <- t(as.matrix(rc.integrated@meta.data[,grep("^Region", colnames(rc.integrated@meta.data))]))
In [ ]:
table(gRNA_scheme[1,])
In [ ]:
apply(gRNA_scheme,1,table)[,"Region_99"]
In [ ]:
output <- lapply(rownames(gRNA_scheme), runSeuratTest, object = rc.integrated, covariate = ngenes)
output <- do.call(rbind, output)
In [ ]:
TAP_DE <- rbind(TAP_DE, output)
write.csv(TAP_DE, "./TAP_DE_aaf800_SCT_202212.csv", row.names=F)

Output¶

In [5]:
TAP_DE <- read.csv("./TAP_DE_aaf800_SCT_202212.csv")
br_anno <- read.table("../../CW_data/Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(rc.integrated@meta.data))),]
In [6]:
adj_pval <- as_tibble(TAP_DE) %>% dplyr::select(gene, ident, p_val_adj) %>% pivot_wider(names_from = ident, values_from = p_val_adj, values_fill = 1)
In [109]:
write.table(adj_pval, "adj_pvalue_mtx_aaf800_SCT_202212.txt", quote = FALSE, row.names = FALSE, sep="\t")
In [7]:
TAP_DE$significance <- TAP_DE$p_val_adj
TAP_DE$significance[which(TAP_DE$p_val_adj < 0.05)] = "<0.05" 
TAP_DE$significance[which(TAP_DE$p_val_adj >= 0.05)] = ">=0.05"

Number of gene per cell/ Number of cell per gene¶

In [111]:
sct <- as.matrix(rc.integrated@assays$SCT@data)
In [112]:
summary(colSums(sct))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   29.60   32.75   32.96   36.19   53.66 
In [113]:
boxplot(colSums(sct))
In [114]:
## Captured genes per cell
summary(colSums(sct>0))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      4      15      17      17      19      29 
In [115]:
boxplot(colSums(sct>0))
In [116]:
## Cells per gene
summary(rowSums(sct>0))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    3.0   172.5  1227.0  4765.3  8414.0 16535.0 
In [117]:
nc <- rowSums(sct>0)
In [118]:
names(nc) <- rownames(sct)
In [119]:
## Number of cells per gene
#sort(nc)
summary(nc)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    3.0   172.5  1227.0  4765.3  8414.0 16535.0 
In [120]:
## Genes that are expressed in less than 50 cells
sort(nc[which(nc < 50)])
AC111006.1
3
AC108210.1
6
LINC02475
11
TLR10
12
YIPF7
16
AC024022.1
18
RPL12P20
24
UCHL1.AS1
28
AC096734.2
32
AC105389.3
32
UCHL1
33
ZBTB12BP
38
In [121]:
boxplot(nc)
In [122]:
dat <- data.frame(gene=names(nc), number_of_cells=as.numeric(nc))
In [123]:
dat <- dat %>% arrange(desc(number_of_cells))
In [124]:
dat <- within(dat, gene <- factor(gene, levels= names(sort(nc,decreasing = FALSE))))
In [125]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=number_of_cells)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Nr of cells in which expression is detected")+ coord_flip() + scale_y_continuous(labels = comma, breaks=c(0,5000,10000,15000,20000))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

Combinatorial effect¶

In [126]:
## APBB2 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="APBB2") %>% filter (significance=="<0.05")
A data.frame: 3 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
4.906618e-040.02617787NANA2.894905e-02APBB2Region_174MAST.cov 18<0.05
3.544565e-150.02304408NANA2.091293e-13APBB2Region_233MAST.cov187<0.05
1.301152e-290.04381527NANA7.676797e-28APBB2Region_52 MAST.cov 98<0.05
In [127]:
## CHRNA9 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="CHRNA9") %>% filter (significance=="<0.05")
A data.frame: 4 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
3.809137e-06 2.931564e-03NANA2.247391e-04CHRNA9Region_250MAST.cov 52<0.05
1.307263e-03-1.274773e-06NANA2.570951e-02CHRNA9Region_663MAST.cov131<0.05
1.283842e-05 1.182990e-03NANA7.574667e-04CHRNA9Region_668MAST.cov 50<0.05
2.797089e-10 1.815131e-03NANA1.650283e-08CHRNA9Region_679MAST.cov105<0.05
In [128]:
## LINC00682 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="LINC00682") %>% filter (significance=="<0.05")
A data.frame: 5 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
8.232078e-04 0.29052319NANA4.856926e-02LINC00682Region_362MAST.cov 37<0.05
2.531771e-07-0.05617795NANA7.468725e-06LINC00682Region_530MAST.cov550<0.05
1.250357e-04-0.07342540NANA3.688555e-03LINC00682Region_537MAST.cov369<0.05
3.373659e-04 0.11022913NANA9.952295e-03LINC00682Region_553MAST.cov 88<0.05
4.408327e-11 0.13827910NANA2.600913e-09LINC00682Region_564MAST.cov181<0.05
In [129]:
## BEND4 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="BEND4") %>% filter (significance=="<0.05")
A data.frame: 4 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
1.804165e-160.05449940NANA 1.064458e-14BEND4Region_669MAST.cov 67<0.05
4.539835e-1640.23330717NANA2.678503e-162BEND4Region_671MAST.cov266<0.05
2.426224e-090.03702678NANA 1.431472e-07BEND4Region_730MAST.cov 97<0.05
1.608772e-030.01909721NANA 4.745879e-02BEND4Region_740MAST.cov144<0.05
In [130]:
zmtx <- matrix(0, 4, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_669=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_671=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_730=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_740=="perturbed"))]=1
In [131]:
idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)
## 574 cells have only one region perturbed, 0 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)
574
0
In [132]:
gene_name <- "BEND4"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 426.33, df = 1, p-value < 2.2e-16
In [133]:
summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.0000  0.0000  0.1649  0.0000  3.1781 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.0000  0.0000  0.7891  1.3863  4.2195 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
                                                
In [134]:
wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 6061126, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
In [135]:
## SHISA3 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="SHISA3") %>% filter (significance=="<0.05")
A data.frame: 15 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
1.706291e-040.06587107NANA1.006712e-02SHISA3Region_729MAST.cov126<0.05
4.558646e-040.07869602NANA1.344801e-02SHISA3Region_730MAST.cov 97<0.05
3.427523e-050.08552611NANA2.022239e-03SHISA3Region_738MAST.cov119<0.05
7.184807e-120.11627863NANA4.239036e-10SHISA3Region_740MAST.cov144<0.05
1.635408e-080.11050001NANA9.648908e-07SHISA3Region_741MAST.cov 91<0.05
2.198444e-070.15529873NANA1.297082e-05SHISA3Region_780MAST.cov 12<0.05
1.630724e-040.21047513NANA9.621269e-03SHISA3Region_789MAST.cov 19<0.05
8.211968e-860.69050674NANA4.845061e-84SHISA3Region_790MAST.cov182<0.05
2.704311e-050.07050796NANA1.595544e-03SHISA3Region_803MAST.cov138<0.05
7.693940e-060.11021861NANA4.539425e-04SHISA3Region_806MAST.cov108<0.05
1.231370e-040.17262495NANA7.265086e-03SHISA3Region_816MAST.cov 43<0.05
2.812233e-080.10472029NANA1.659218e-06SHISA3Region_828MAST.cov 79<0.05
1.644173e-200.33153781NANA9.700622e-19SHISA3Region_829MAST.cov 49<0.05
9.455928e-120.27819800NANA5.578998e-10SHISA3Region_831MAST.cov 50<0.05
1.126435e-050.10038970NANA6.645969e-04SHISA3Region_840MAST.cov106<0.05
In [136]:
zmtx <- matrix(0, 15, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_729=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_730=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_738=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_740=="perturbed"))]=1
zmtx[5,which((rc.integrated$Region_741=="perturbed"))]=1
zmtx[6,which((rc.integrated$Region_780=="perturbed"))]=1
zmtx[7,which((rc.integrated$Region_789=="perturbed"))]=1
zmtx[8,which((rc.integrated$Region_790=="perturbed"))]=1
zmtx[9,which((rc.integrated$Region_803=="perturbed"))]=1
zmtx[10,which((rc.integrated$Region_806=="perturbed"))]=1
zmtx[11,which((rc.integrated$Region_816=="perturbed"))]=1
zmtx[12,which((rc.integrated$Region_828=="perturbed"))]=1
zmtx[13,which((rc.integrated$Region_829=="perturbed"))]=1
zmtx[14,which((rc.integrated$Region_831=="perturbed"))]=1
zmtx[15,which((rc.integrated$Region_840=="perturbed"))]=1
In [137]:
idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)
## 1363 cells have only one region perturbed, 0 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)
1363
0
In [138]:
gene_name <- "SHISA3"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 386.73, df = 1, p-value < 2.2e-16
In [139]:
summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.332   0.000   4.663 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.861   1.609   4.812 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
                                                
In [140]:
wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 12859113, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
In [141]:
## PHOX2B expression
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="PHOX2B") %>% filter (significance=="<0.05")
A data.frame: 13 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
5.421915e-06 0.4677258NANA3.198930e-04PHOX2BRegion_477MAST.cov116<0.05
5.047705e-25-0.5493911NANA2.978146e-23PHOX2BRegion_494MAST.cov559<0.05
2.347806e-04 0.3603152NANA1.385206e-02PHOX2BRegion_504MAST.cov140<0.05
7.485219e-05-0.3404573NANA4.416279e-03PHOX2BRegion_512MAST.cov133<0.05
1.558321e-04 0.4048890NANA9.194094e-03PHOX2BRegion_520MAST.cov169<0.05
1.427880e-12-0.3854239NANA8.424490e-11PHOX2BRegion_530MAST.cov550<0.05
7.026451e-16-0.3656320NANA4.145606e-14PHOX2BRegion_537MAST.cov369<0.05
9.920086e-11 0.8111515NANA5.852851e-09PHOX2BRegion_553MAST.cov 88<0.05
2.434311e-06 0.6284872NANA1.436244e-04PHOX2BRegion_557MAST.cov130<0.05
7.928104e-14 0.5063157NANA4.677581e-12PHOX2BRegion_561MAST.cov285<0.05
1.676852e-05-0.2376408NANA9.893427e-04PHOX2BRegion_562MAST.cov370<0.05
1.151785e-08 0.4317661NANA3.397765e-07PHOX2BRegion_564MAST.cov181<0.05
9.708373e-06-0.5605712NANA5.727940e-04PHOX2BRegion_99 MAST.cov 70<0.05
In [142]:
zmtx <- matrix(0, 13, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_477=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_494=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_504=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_512=="perturbed"))]=1
zmtx[5,which((rc.integrated$Region_520=="perturbed"))]=1
zmtx[6,which((rc.integrated$Region_530=="perturbed"))]=1
zmtx[7,which((rc.integrated$Region_537=="perturbed"))]=1
zmtx[8,which((rc.integrated$Region_553=="perturbed"))]=1
zmtx[9,which((rc.integrated$Region_557=="perturbed"))]=1
zmtx[10,which((rc.integrated$Region_561=="perturbed"))]=1
zmtx[11,which((rc.integrated$Region_562=="perturbed"))]=1
zmtx[12,which((rc.integrated$Region_564=="perturbed"))]=1
zmtx[13,which((rc.integrated$Region_99=="perturbed"))]=1
In [143]:
idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)
In [144]:
## 3152 cells have only one region perturbed, 4 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)
3152
4
In [145]:
gene_name <- "PHOX2B"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + geom_boxplot(outlier.shape=NA)+ coord_cartesian(ylim=c(-4,9))+theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 234.03, df = 2, p-value < 2.2e-16
In [146]:
gene_name <- "PHOX2B"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 234.03, df = 2, p-value < 2.2e-16
In [147]:
pdf("PHOX2B_combinatorial_effect_wo_outliers_202212.pdf",width=6,height=6)
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [148]:
summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.6931  1.9459  1.7839  2.8332  4.7791 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.099   2.485   2.164   3.219   4.868 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   1.354   1.501   2.855   3.296 
In [149]:
wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 24749532, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
In [150]:
wilcox.test(dat$expression_level[which(dat$region_targeted==">1 region")], dat$expression_level[which(dat$region_targeted=="Others")])
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == ">1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 24284, p-value = 0.7473
alternative hypothesis: true location shift is not equal to 0
In [151]:
wilcox.test(dat$expression_level[which(dat$region_targeted==">1 region")], dat$expression_level[which(dat$region_targeted=="1 region")])
	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == ">1 region")] and dat$expression_level[which(dat$region_targeted == "1 region")]
W = 4811.5, p-value = 0.4111
alternative hypothesis: true location shift is not equal to 0
In [152]:
ggplot(TAP_DE[grep("^Region", TAP_DE$ident),], aes(x=avg_logFC, y=-log(p_val_adj,10))) + geom_point(aes(colour = significance),size=3)+theme_classic()+xlab("Fold Change (log)")+ylab("Adj-p-value (-log10)")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
Warning message:
“Removed 3703 rows containing missing values (`geom_point()`).”
In [153]:
pdf("Rhapsody_region_summary_202212.pdf",width=6,height=6)
ggplot(TAP_DE[grep("^Region", TAP_DE$ident),], aes(x=avg_logFC, y=-log(p_val_adj,10))) + geom_point(aes(colour = significance),size=3)+theme_classic()+xlab("Fold Change (log)")+ylab("Adj-p-value (-log10)")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
Warning message:
“Removed 3703 rows containing missing values (`geom_point()`).”
png: 2
In [154]:
## 1034/1046 gRNA, 222 Region
length(table(TAP_DE[grep("^X",TAP_DE$ident),]$ident))
length(table(TAP_DE[grep("^Region",TAP_DE$ident),]$ident))
1034
222
In [155]:
# Missing gRNA
1046-length(table(TAP_DE$ident[grep("^X",TAP_DE$ident)]))
12
In [156]:
# ncells per gRNA/bin/region (control gRNAs excluded)
summary(TAP_DE$ncells[grep("^X",TAP_DE$ident)], breaks = 100)
#summary(TAP_DE$ncells[grep("^PHOX",TAP_DE$ident)], breaks = 100)
summary(TAP_DE$ncells[grep("^Region",TAP_DE$ident)], breaks = 100)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   4.00   13.00   16.00   16.99   21.00   50.00 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   7.00   39.00   61.00   76.37   90.00  559.00 
In [8]:
# Significance level 0.05
hits <- TAP_DE %>% filter(method=="MAST.cov") %>% filter(p_val_adj < 0.05)
ghits <- hits[grep("^X",hits$ident),]
#bhits <- hits[grep("^PHOX", hits$ident),]
rhits <- hits[grep("^Region", hits$ident),]
In [158]:
# number of DE genes
length(table(ghits$gene))
#length(table(bhits$gene))
length(table(rhits$gene))
44
33
In [159]:
length(unique(rhits$ident))
60
In [160]:
sum(table(rhits$ident)>1)
22
In [161]:
table(ghits$gene)
AC095057.3 AC096586.1 AC098590.1 AC098591.1 AC098591.2 AC105389.1 AC105389.3 
         3          5          3          4          3          6          1 
AC108471.2      APBB2    ARL4AP2   ATP1B1P1     ATP8A1      BEND4     CHRNA9 
         2          9          3          3          6         20          9 
   DCAF4L1   FAM114A1     GNPDA2       GUF1      KLHL5   KRT18P25       LIAS 
         1          1          4          2          1          8          5 
    LIMCH1  LINC00682  LINC02265      N4BP2  NDUFB4P12      NSUN7   PABPC1P1 
         2          8          3          3          6          4          6 
     PDS5A     PHOX2B      RBM47       RFC1     RPS7P7     SHISA3    SLC30A9 
         2         20          4          2          3         30          2 
    SMIM14       TLR1       TLR6    TMEM156     TMEM33  UCHL1.AS1       UGDH 
         2          6          2          4          1          1          3 
     WDR19   ZBTB12BP 
         4          1 
In [162]:
# sig pairs
nrow(ghits)
#nrow(bhits)
nrow(rhits)
218
92
In [163]:
PHOX2B_ghits <- ghits %>% filter(gene=="PHOX2B")
#PHOX2B_bhits <- bhits %>% filter(gene=="PHOX2B")
PHOX2B_rhits <- rhits %>% filter(gene=="PHOX2B")
In [164]:
PHOX2B_rhits
A data.frame: 13 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
5.421915e-06 0.4677258NANA3.198930e-04PHOX2BRegion_477MAST.cov116<0.05
5.047705e-25-0.5493911NANA2.978146e-23PHOX2BRegion_494MAST.cov559<0.05
2.347806e-04 0.3603152NANA1.385206e-02PHOX2BRegion_504MAST.cov140<0.05
7.485219e-05-0.3404573NANA4.416279e-03PHOX2BRegion_512MAST.cov133<0.05
1.558321e-04 0.4048890NANA9.194094e-03PHOX2BRegion_520MAST.cov169<0.05
1.427880e-12-0.3854239NANA8.424490e-11PHOX2BRegion_530MAST.cov550<0.05
7.026451e-16-0.3656320NANA4.145606e-14PHOX2BRegion_537MAST.cov369<0.05
9.920086e-11 0.8111515NANA5.852851e-09PHOX2BRegion_553MAST.cov 88<0.05
2.434311e-06 0.6284872NANA1.436244e-04PHOX2BRegion_557MAST.cov130<0.05
7.928104e-14 0.5063157NANA4.677581e-12PHOX2BRegion_561MAST.cov285<0.05
1.676852e-05-0.2376408NANA9.893427e-04PHOX2BRegion_562MAST.cov370<0.05
1.151785e-08 0.4317661NANA3.397765e-07PHOX2BRegion_564MAST.cov181<0.05
9.708373e-06-0.5605712NANA5.727940e-04PHOX2BRegion_99 MAST.cov 70<0.05

#CaRE vs #gene¶

In [165]:
table(table(ghits$ident))
  1   2   3   5 
147  23   5   2 
In [166]:
par(mar = c(5, 5, 2, 2))
barplot(table(table(ghits$ident)), xlab="number of differentially expressed gene", ylab="number of gRNA", cex.lab=1.5)
cat("gRNA that regulates 2 genes")
names(which(table(ghits$ident)==2))
cat("gRNA that regulates 3 genes")
names(which(table(ghits$ident)==3))
gRNA that regulates 2 genes
  1. 'X124'
  2. 'X173'
  3. 'X214'
  4. 'X283'
  5. 'X341'
  6. 'X350'
  7. 'X356'
  8. 'X380'
  9. 'X404'
  10. 'X572'
  11. 'X624'
  12. 'X634'
  13. 'X651'
  14. 'X698'
  15. 'X717'
  16. 'X74'
  17. 'X780'
  18. 'X854'
  19. 'X882'
  20. 'X893'
  21. 'X936'
  22. 'X942'
  23. 'X977'
gRNA that regulates 3 genes
  1. 'X185'
  2. 'X512'
  3. 'X58'
  4. 'X829'
  5. 'X886'
In [167]:
ggplot(data.frame(table(table(ghits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of gRNA")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [168]:
pdf("number_of_DE_per_gRNA_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(ghits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of gRNA")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2
In [169]:
data.frame(table(table(rhits$gene)))
A data.frame: 7 × 2
Var1Freq
<fct><int>
1 14
2 8
3 4
4 3
5 2
13 1
15 1
In [170]:
table(rhits$gene)
AC095057.3 AC096586.1 AC096586.2 AC096734.2 AC098590.1 AC098591.1 AC105389.1 
         1          1          1          1          1          1          1 
     APBB2    ARL4AP2     ATP8A1      BEND4     CHRNA9     GNPDA2   KRT18P25 
         3          2          3          4          4          2          3 
 LINC00682  LINC02265      N4BP2  NDUFB4P12      NSUN7   PABPC1P1      PDS5A 
         5          4          1          2          2          2          1 
    PHOX2B      RBM47     RPS7P7     SHISA3    SLC30A9       TLR1       TLR6 
        13          1          5         15          2          3          2 
   TMEM156     TMEM33       UGDH      WDR19   ZBTB12BP 
         2          1          1          1          1 
In [171]:
data.frame(table(table(rhits$ident)))
A data.frame: 5 × 2
Var1Freq
<fct><int>
138
215
3 5
4 1
5 1
In [172]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(data.frame(table(table(rhits$gene))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Number of CaREs")+ylab("Number of differentially expressed gene")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [173]:
pdf("number_of_region_per_DE_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(rhits$gene))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Number of CaREs")+ylab("Number of differentially expressed gene")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2
In [174]:
ggplot(data.frame(table(table(rhits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of CaREs")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [175]:
pdf("number_of_DE_per_region_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(rhits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of CaREs")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2
In [176]:
# New
barplot(table(table(rhits$ident)), xlab="number of differentially expressed gene", ylab="numer of regions", cex.lab=1.5)
cat("region that regulates 2 genes")
names(which(table(rhits$ident)==2))
region that regulates 2 genes
  1. 'Region_132'
  2. 'Region_3'
  3. 'Region_33'
  4. 'Region_494'
  5. 'Region_530'
  6. 'Region_537'
  7. 'Region_553'
  8. 'Region_65'
  9. 'Region_671'
  10. 'Region_679'
  11. 'Region_729'
  12. 'Region_730'
  13. 'Region_740'
  14. 'Region_935'
  15. 'Region_99'

nr genes/CaRE & nr CaRE/genes (On average, one gene/CaRE regulates one gene's exp)¶

In [177]:
dat <- data.frame(treatment=rep("gRNA", length(as.numeric(table(ghits$ident)))), nr_gene_per_CaRE=as.numeric(table(ghits$ident)))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(as.numeric(table(bhits$ident)))), nr_gene_per_CaRE=as.numeric(table(bhits$ident))))
dat <- rbind(dat, data.frame(treatment=rep("region", length(as.numeric(table(rhits$ident)))), nr_gene_per_CaRE=as.numeric(table(rhits$ident))))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","region")))
In [178]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nr_gene_per_CaRE)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [179]:
pdf("nr_gene_per_CaRE_2_counts_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nr_gene_per_CaRE)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [180]:
##On average, one gene/CaRE regulates one gene's exp
cat("gRNA")
summary(as.numeric(table(ghits$ident)))
#cat("bin")
#summary(as.numeric(table(bhits$ident)))
cat("region")
summary(as.numeric(table(rhits$ident)))
gRNA
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.232   1.000   5.000 
region
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.533   2.000   5.000 
In [181]:
## 22 CaRE regulates more than 1 gene's exp
length(which(as.numeric(table(rhits$ident))>1))
22
In [182]:
dat <- data.frame(treatment=rep("gRNA", length(as.numeric(table(ghits$gene)))), nr_CaRE_per_gene=as.numeric(table(ghits$gene)))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(as.numeric(table(bhits$gene)))), nr_CaRE_per_gene=as.numeric(table(bhits$gene))))
dat <- rbind(dat, data.frame(treatment=rep("region", length(as.numeric(table(rhits$gene)))), nr_CaRE_per_gene=as.numeric(table(rhits$gene))))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","region")))
In [183]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [184]:
pdf("nr_CaRE_per_gene_2counts_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [185]:
dat_g <- dat %>% filter(treatment=="gRNA")
dat_r <- dat %>% filter(treatment=="region")
In [186]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat_g, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [187]:
pdf("nr_CaRE_per_gene_2counts_gRNA_202212.pdf",width=6,height=6)
ggplot(dat_g, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [188]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat_r, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [189]:
pdf("nr_CaRE_per_gene_2counts_region_202212.pdf",width=6,height=6)
ggplot(dat_r, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [190]:
## On average, a gene is regulated by 2-3 CaREs
cat("gRNA")
summary(as.numeric(table(ghits$gene)))
#cat("bin")
#summary(as.numeric(table(bhits$gene)))
cat("region")
summary(as.numeric(table(rhits$gene)))
gRNA
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   2.000   3.000   4.955   6.000  30.000 
region
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   2.000   2.788   3.000  15.000 
In [191]:
dat <- data.frame(care = names(sort(table(ghits$ident),decreasing = FALSE)), nr_gene = as.numeric(sort(table(ghits$ident),decreasing = FALSE)))
dat <- within(dat, care <- factor(care, levels= names(sort(table(ghits$ident),decreasing = FALSE))))
In [192]:
nrow(dat)
177
In [193]:
dat <- dat[162:177,]
In [194]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [195]:
pdf("DE_gRNA_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [196]:
dat <- data.frame(care = names(sort(table(rhits$ident),decreasing = FALSE)), nr_gene = as.numeric(sort(table(rhits$ident),decreasing = FALSE)))
dat <- within(dat, care <- factor(care, levels= names(sort(table(rhits$ident),decreasing = FALSE))))
In [197]:
nrow(dat)
60
In [198]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [199]:
pdf("DE_region_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [200]:
dat <- data.frame(gene = names(sort(table(ghits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(ghits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(ghits$gene),decreasing = FALSE))))
In [201]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant gRNAs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [202]:
pdf("DE_gRNA_gene_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant gRNAs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [203]:
dat <- data.frame(gene = names(sort(table(rhits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(rhits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(rhits$gene),decreasing = FALSE))))
In [204]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [205]:
pdf("DE_region_gene_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [206]:
## Genes having less than 50 genes expressed
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC108210.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="Y1PF7") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="RPL12P20") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="UCHL1.AS1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="UCHL1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="LINC02475") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="TLR10") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC024022.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC105389.3") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC111006.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC096734.2") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="ZBTB12BP") %>% filter (significance=="<0.05")
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 0 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
A data.frame: 1 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
0.00029736450.0001065904NANA0.01754451AC096734.2Region_847MAST.cov76<0.05
A data.frame: 1 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
0.00045379730.0006368986NANA0.01338702ZBTB12BPRegion_729MAST.cov126<0.05
In [ ]:

In [98]:
dat <- data.frame(gene = names(sort(table(rhits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(rhits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(rhits$gene),decreasing = FALSE))))
In [10]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [99]:
genes.bed$order <- seq(1,129)
In [100]:
sg <- genes.bed[match(c("TLR10","TLR1","TLR6","FAM114A1","TMEM156","KLHL5","AC079921.2","WDR19","RFC1","LIAS","AC021148.1","UGDH","SMIM14","AC108471.2","UBE2K",
                 "ZBTB12BP","AC098591.1","AC098591.2","PABPC1P1","PDS5A","KRT18P25","N4BP2","AC095057.3","LINC02265","CHRNA9","RBM47","NSUN7","ARL4AP2","APBB2",
                 "UCHL1","UCHL1.AS1","LIMCH1","RPL12P20","AC105389.3","PHOX2B","AC105389.1","LINC00682","AC108210.1","TMEM33","DCAF4L1","AC106052.1","SLC30A9",
                 "ATP1B1P1","AC111006.1","BEND4","AC024022.1","SHISA3","RPS7P7","ATP8A1","AC096734.2","AC096734.1","AC098590.1","NDUFB4P12","LINC02475","GUF1",
                 "YIPF7","AC096586.2","AC096586.1","GNPDA2"),genes.bed$gene),]
In [101]:
sg$order <- seq(1,59)
In [102]:
dat <- left_join(sg, dat, by="gene") %>% arrange(order)
In [103]:
dat$gene <- factor(dat$gene, levels = dat$gene)
In [104]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
Warning message:
“Removed 26 rows containing missing values (`position_stack()`).”
In [105]:
## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=8, repr.plot.height=12)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 0, hjust = 1)) )
    
}
In [106]:
annotation <- c()
value <- c()
group <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")],rc.integrated@assays$SCT@data[i,which(rc.integrated$X1!="control")])
    group <- c(group, rep("Control",length(which(rc.integrated$X1=="control"))), rep("Perturbed",length(which(rc.integrated$X1!="control"))))                                               
}


annotation <- factor(annotation, levels= dat$gene)
group <- factor(group, levels= c("Perturbed", "Control"))
In [107]:
plot_box(annotation, value, group, "Normalized Gene Expression Level")
In [109]:
summary(rowSums(rc.integrated@assays$SCT@data))
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
    2.08   146.73  1112.80  9238.29  9419.16 78267.55 
In [241]:
## Define high and low expressed genes, coding and non-coding genes
high_exp_genes <- c("FAM114A1","KLHL5","WDR19","RFC1","LIAS","UGDH","SMIM14","UBE2K","AC098591.1","PDS5A","KRT18P25","N4BP2",
                    "ARL4AP2","APBB2","LIMCH1","PHOX2B","LINC00682","TMEM33","SLC30A9","SHISA3","RPS7P7","ATP8A1","AC098590.1",
                    "NDUFB4P12","GUF1","AC096586.1","GNPDA2")
low_exp_genes <- c("TLR10","TLR1","TLR6","TMEM156","AC079921.2","AC021148.1","AC108471.2","ZBTB12BP","AC098591.2","PABPC1P1",
                  "AC095057.3","LINC02265","CHRNA9","RBM47","NSUN7","UCHL1","UCHL1.AS1","RPL12P20","AC105389.3","AC105389.1",
                  "AC108210.1","DCAF4L1","AC106052.1","ATP1B1P1","AC111006.1","BEND4","AC024022.1","AC096734.2","AC096734.1",
                   "LINC02475","YIPF7","AC096586.2")
coding_genes <- c("TLR10","TLR1","TLR6","FAM114A1","TMEM156","KLHL5","WDR19","RFC1","LIAS","UGDH","SMIM14","UBE2K",
                 "PDS5A","N4BP2","CHRNA9","RBM47","NSUN7","APBB2","UCHL1","LIMCH1","PHOX2B","TMEM33","DCAF4L1","SLC30A9",
                 "BEND4","SHISA3","ATP8A1","GUF1","YIPF7","GNPDA2")
## Including pseudogenes
non_coding_genes <- c("AC098591.1", "AC098590.1", "AC096586.1", "AC079921.2", "AC021148.1", "AC108471.2", "AC098591.2", "AC095057.3",
                      "AC105389.3", "AC105389.1", "AC108210.1", "AC106052.1", "AC111006.1", "AC024022.1", "AC096734.2", "AC096734.1",
                      "AC096586.2", "LINC02475", "LINC00682", "LINC02265", "ATP1B1P1", "PABPC1P1", "NDUFB4P12", "ARL4AP2", "UCHL1.AS1",
                      "RPL12P20", "RPS7P7", "ZBTB12BP", "KRT18P25")
In [114]:
length(low_exp_genes)
32
In [115]:
length(high_exp_genes)
27
In [242]:
length(coding_genes)
30
In [240]:
length(non_coding_genes)
29
In [19]:
dat <- dat %>% filter(nr_care != "NA")
In [20]:
options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [25]:
pdf("DE_region_gene_2counts_20240528.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [21]:
dat
A data.frame: 33 x 9
chromstartstopgenescorestrandtypeordernr_care
<chr><dbl><dbl><fct><chr><chr><chr><int><dbl>
chr43879067638856817TLR1 .-gene 2 3
chr43882371438856817TLR6 .-gene 3 2
chr43896674339032922TMEM156 .-gene 5 2
chr43918250339285810WDR19 .+gene 8 1
chr43949875439528311UGDH .-gene12 1
chr43977008039771371ZBTB12BP .-gene16 1
chr44008298240083106AC098591.1.+gene17 1
chr43997344339974338PABPC1P1 .+gene19 2
chr43982286239977956PDS5A .-gene20 1
chr44002023940021517KRT18P25 .+gene21 3
chr44005684940158252N4BP2 .+gene22 1
chr44016667440167831AC095057.3.+gene23 1
chr44031648440330419LINC02265 .+gene24 4
chr44033533240355217CHRNA9 .+gene25 4
chr44042326640630875RBM47 .-gene26 1
chr44074992440811184NSUN7 .+gene27 2
chr44078610940786710ARL4AP2 .+gene28 2
chr44081002641216714APBB2 .-gene29 3
chr44174408141748725PHOX2B .-gene3513
chr44175034441757341AC105389.1.+gene36 1
chr44187274641882955LINC00682 .-gene37 5
chr44193512841960803TMEM33 .+gene39 1
chr44199050142090461SLC30A9 .+gene42 2
chr44211085242152878BEND4 .-gene45 4
chr44239748742402487SHISA3 .+gene4715
chr44247180942472380RPS7P7 .+gene48 5
chr44240837242657105ATP8A1 .-gene49 3
chr44265749542657928AC096734.2.+gene50 1
chr44341004043410937AC098590.1.-gene52 1
chr44389896143899351NDUFB4P12 .+gene53 2
chr44469394544694386AC096586.2.-gene57 1
chr44470440444704965AC096586.1.+gene58 1
chr44468219944726588GNPDA2 .-gene59 2
In [23]:
rc.integrated
An object of class Seurat 
125 features across 16535 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA
In [42]:
annotation <- c()
value <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,])
}
annotation <- factor(annotation, levels= dat$gene)
In [69]:
names(table(pr_anno$prom_name))
  1. 'BEND4'
  2. 'DCAF4L1'
  3. 'NSUN7'
  4. 'PHOX2B'
  5. 'RNU1-49P'
  6. 'RP11-109E24.1'
  7. 'RP11-227F19.1'
  8. 'RP11-227F19.2'
  9. 'RP11-457P14.5'
  10. 'RP11-457P14.6'
  11. 'SHISA3'
  12. 'SLC30A9'
  13. 'TMEM33'
  14. 'UCHL1'
  15. 'UCHL1.AS1'
In [91]:
## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=12, repr.plot.height=8)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  #coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 60, hjust = 1)) )
    
}
In [92]:
intersect(names(table(pr_anno$prom_name)),dat$gene)
  1. 'BEND4'
  2. 'NSUN7'
  3. 'PHOX2B'
  4. 'SHISA3'
  5. 'SLC30A9'
  6. 'TMEM33'
In [93]:
annotation <- c()
value <- c()
group <- c()
for (i in intersect(names(table(pr_anno$prom_name)),dat$gene)){
    pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==i)]],1, function(x) sum(which(x=="perturbed")))>=1))
    pt <- rep("All other", ncol(rc.integrated))
    pt[pos_idx] <- "TSS" 
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))                                  
    group <- c(group, pt)
    value <- c(value, rc.integrated@assays$SCT@data[i,])                                  
}
group <- factor(group, levels= c("All other", "TSS"))
In [94]:
plot_box(annotation, value, group, "Normalized Gene Expression Level")
In [43]:
#ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
#  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
#        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
#                                  #+ coord_cartesian(ylim = c(0, 10))
In [44]:
## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value
    )
    
  options(repr.plot.width=12, repr.plot.height=8)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value)) +
  geom_boxplot() +
  #geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 70, hjust = 1)) )
    
}
In [45]:
plot_box(annotation, value, "Gene Expression Level")
In [46]:
annotation <- c()
value <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,length(which(rc.integrated$X1=="control"))))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")])
}
annotation <- factor(annotation, levels= dat$gene)
In [47]:
plot_box(annotation, value, "Normalized Gene Expression Level")
In [95]:
## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=8, repr.plot.height=12)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 0, hjust = 1)) )
    
}
In [96]:
annotation <- c()
value <- c()
group <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")],rc.integrated@assays$SCT@data[i,which(rc.integrated$X1!="control")])
    group <- c(group, rep("Control",length(which(rc.integrated$X1=="control"))), rep("Perturbed",length(which(rc.integrated$X1!="control"))))                                               
}


annotation <- factor(annotation, levels= dat$gene)
group <- factor(group, levels= c("Perturbed", "Control"))
In [97]:
plot_box(annotation, value, group, "Normalized Gene Expression Level")

Plot TSS.distance¶

In [207]:
head(genes.bed)
A data.frame: 6 × 7
chromstartstopgenescorestrandtype
<chr><dbl><dbl><chr><chr><chr><chr>
1chr43800678338007105MRPS33P2 .-gene
2chr43827617738279880AC098680.2.-gene
3chr43828699338287491AC098680.1.+gene
4chr43836691338385759LINC02513 .+gene
5chr43839075338391675AC024023.1.+gene
6chr43842066138523180LINC01258 .-gene
In [208]:
chrom1 <- br_anno$Chr[match(TAP_DE$ident, br_anno$Rhapsody_name)]
start1 <- br_anno$guide_start[match(TAP_DE$ident, br_anno$Rhapsody_name)]
end1 <- br_anno$guide_end[match(TAP_DE$ident, br_anno$Rhapsody_name)]
chrom2 <- genes.bed$chrom[match(TAP_DE$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(TAP_DE$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(TAP_DE$gene, genes.bed$gene)]
name <- paste0(TAP_DE$ident,"_",TAP_DE$gene)
score <- TAP_DE$avg_logFC
strand1 <- br_anno$strand[match(TAP_DE$ident, br_anno$Rhapsody_name)]
strand2 <- genes.bed$strand[match(TAP_DE$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(TAP_DE$gene))
gene <- TAP_DE$gene
gRNA <- TAP_DE$ident
log_pvaladj <- -log(TAP_DE$p_val_adj)
type <- TAP_DE$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#ALL
TAP_DE.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
#TAP_DE.bedpe <- ghits.bedpe[!is.na(TAP_DE.bedpe$score),]
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$guide_start, stop=br_anno$guide_end, gene=br_anno$Rhapsody_name, score=".", strand=br_anno$strand, type="gene")
In [209]:
TAP_DE.bedpe <- TAP_DE.bedpe[!is.na(TAP_DE.bedpe$chrom1),]
In [210]:
TAP_DE.bedpe$distance.TSS <- apply(TAP_DE.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})
In [211]:
TAP_DE.bedpe$significance <- rep("adj.pval >= 0.05", nrow(TAP_DE.bedpe))
TAP_DE.bedpe$significance[TAP_DE.bedpe$log_pvaladj>1.3] <- "adj.pval < 0.05"
In [212]:
head(TAP_DE.bedpe)
A data.frame: 6 × 17
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtypedistance.TSSsignificance
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr><dbl><chr>
1chr44079001940790039chr44468219944726588X1_GNPDA2 -0.015279653+-26GNPDA2 X10.008408941down_regulated3936569adj.pval >= 0.05
2chr44079001940790039chr44247180942472380X1_RPS7P7 0.133542942++44RPS7P7 X10.008408941up_regulated 1681790adj.pval >= 0.05
3chr44079001940790039chr44033533240355217X1_CHRNA9 0.001029732++23CHRNA9 X10.008408941up_regulated 454687adj.pval >= 0.05
4chr44079001940790039chr43904503839126857X1_KLHL5 0.012400904++28KLHL5 X10.008408941up_regulated 1744981adj.pval >= 0.05
5chr44079001940790039chr44016667440167831X1_AC095057.3 NA++ 4AC095057.3X10.008408941NA 623345adj.pval >= 0.05
6chr44079001940790039chr44174408141748725X1_PHOX2B -0.001536993+-40PHOX2B X10.008408941down_regulated 958706adj.pval >= 0.05
In [213]:
head(pr_anno)
A data.frame: 6 × 10
chrstartendstrandnamechr_promstart_promend_promprom_nameoverlap
<chr><int><int><chr><chr><chr><int><int><chr><int>
1chr44075020440750224+X396chr44074939640750396NSUN7 20
2chr44125612041256140+X486chr44125591241256912UCHL1 20
3chr44125613341256153+X487chr44125591241256912UCHL1 20
4chr44125659941256619+X488chr44125622641257226UCHL1.AS120
5chr44125659941256619+X488chr44125591241256912UCHL1 20
6chr44125661141256631+X489chr44125622641257226UCHL1.AS120
In [214]:
TAP_DE.bedpe_pr <- full_join(TAP_DE.bedpe, rename(pr_anno, gRNA = name), by = "gRNA")
TAP_DE.bedpe_pr_en <- TAP_DE.bedpe_pr[!is.na(TAP_DE.bedpe_pr$prom_name),] %>% filter(significance=="adj.pval < 0.05") %>% filter(prom_name!=gene)
## 21 gRNA
table(TAP_DE.bedpe_pr_en$gRNA)
X1019  X237  X486  X490  X624  X631  X634  X635  X636  X672  X823  X826  X849 
    1     1     1     1     1     2     8     1     1     3     4     1     1 
 X850  X912  X913  X914  X915 
    3     1     1     3     3 
In [215]:
## Region
table(br_anno$Region_name[match(TAP_DE.bedpe_pr_en$gRNA, br_anno$Rhapsody_name)])
Region_256 Region_494 Region_504 Region_577 Region_582 Region_603 Region_609 
         2         13          3          4          1          1          1 
Region_671 Region_790 
         4          8 
In [216]:
## Check whether genes fall into the genome range covered by gRNA targeting
gRNA_MIN <- min(TAP_DE.bedpe$start1)
gRNA_MAX <- max(TAP_DE.bedpe$end1)
TAP_DE.bedpe$gRNA_covered <- apply(TAP_DE.bedpe, 1, function(x){if(x[5]<=gRNA_MIN & x[6]<= gRNA_MIN){"Not Covered"}else if(x[5]>=gRNA_MAX & x[6]>=gRNA_MAX){"Not Covered"}else {"Covered"}})
In [217]:
table(TAP_DE.bedpe$gRNA_covered)
    Covered Not Covered 
      25850       35156 
In [218]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(TAP_DE.bedpe, aes(distance.TSS/1000000, log_pvaladj, shape=significance)) +geom_point(aes(colour = gRNA_covered),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="gRNA")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [219]:
pdf("Distance_to_TSS_vs_pvalue_gRNA_coverage_202212.pdf",width=8,height=6)
ggplot(TAP_DE.bedpe, aes(distance.TSS/1000000, log_pvaladj, shape=significance)) +geom_point(aes(colour = gRNA_covered),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="gRNA")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2

Sushi¶

In [283]:
source('plotBedpe.R')
source('convertstrandinfo.R')
source('SushiColors.R')
In [117]:
ghits <- hits[grep("^X",hits$ident),]
In [118]:
chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Rhapsody_name)]
start1 <- br_anno$guide_start[match(ghits$ident, br_anno$Rhapsody_name)]
end1 <- br_anno$guide_end[match(ghits$ident, br_anno$Rhapsody_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
name <- paste0(ghits$ident,"_",ghits$gene)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Rhapsody_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$guide_start, stop=br_anno$guide_end, gene=br_anno$Rhapsody_name, score=".", strand=br_anno$strand, type="gene")
In [119]:
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()%>% arrange(gene)
In [287]:
nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000
In [288]:
getwd()
'/fast/AG_Ohler/CheWei/kallisto-bus/Dusa_hg38_p13'
In [289]:
#Type
pdf("track_regulation_grna_202212.pdf",width=16,height=4)
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
[1] "yes"
png: 2
In [290]:
#Log_FoldChange
pdf("track_avg_logFC_grna_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
[1] "yes"
png: 2
In [291]:
#GeneTrack
pdf("track_gene_grna_202212.pdf",width=16,height=2.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
png: 2
In [292]:
#gRNATRACK
pdf("track_grna_grna_202212.pdf",width=16,height=8)
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
png: 2
In [293]:
#pvalue_adjusted
#options(repr.plot.width=16, repr.plot.height=2)
#par(mar = c(0, 4, 2, 4))
#pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
#heights = ghits.bedpe$log_pvaladj,plottype="loops",
#colorby=ghits.bedpe$samplenumber,
#colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=TRUE))
#lwdby=ghits.bedpe$score
#axis(side=2,las=2,tcl=.2)
#mtext("log(adj_p_value)",side=2,line=3,cex=1,font=2)
#Type
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

Classify promoters¶

In [120]:
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})
In [121]:
pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
In [122]:
table(dat$gene)
    NA SHISA3 
   206      5 
In [123]:
ghits.bedpe %>% filter(promoter!="NA")
A data.frame: 5 x 17
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtypedistance.TSSpromoter
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr><dbl><chr>
chr44239744742397467chr44239748742402487X910_SHISA30.4664096++34SHISA3X910 4.527663up_regulated 40SHISA3
chr44239751542397535chr44239748742402487X912_SHISA30.9427664++34SHISA3X91263.549336up_regulated 28SHISA3
chr44239761142397631chr44239748742402487X913_SHISA30.9012685++34SHISA3X91316.047242up_regulated124SHISA3
chr44239764142397661chr44239748742402487X914_SHISA31.3704953++34SHISA3X91483.873479up_regulated154SHISA3
chr44239767942397699chr44239748742402487X915_SHISA30.6755128++34SHISA3X91555.427103up_regulated192SHISA3

Jumped genes¶

In [124]:
ghits.bedpe
A data.frame: 211 x 17
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtypedistance.TSSpromoter
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr><dbl><chr>
1chr44125942841259448chr44467841944700928X1002_GUF1 0.0341733215++18GUF1 X1002 4.905729up_regulated 3418991NA
2chr44219418542194205chr44341004043410937X1027_AC098590.1-0.2919132455+- 3AC098590.1X1027 4.115792down_regulated1216752NA
3chr44136793041367950chr43904503839126857X108_KLHL5 -0.0010774513++19KLHL5 X108 2.996921down_regulated2322892NA
4chr44139552841395548chr44002023940021517X117_KRT18P25 0.0354084092++20KRT18P25 X117 4.639459up_regulated 1375289NA
5chr44140561441405634chr43945900339485109X120_LIAS 0.0044690703++21LIAS X120 3.831877up_regulated 1946611NA
6chr44140562541405645chr44187274641882955X121_LINC00682 -0.1359951890+-23LINC00682 X121 3.043304down_regulated 477330NA
7chr44141428041414300chr44122007341256727X124_UCHL1.AS1 0.0100892920+-41UCHL1.AS1 X124 3.004131up_regulated 157553NA
8chr44141428041414300chr44016667440167831X124_AC095057.3 0.0008032585++ 1AC095057.3X124 3.004131up_regulated 1247606NA
9chr44149477641494796chr43879067638856817X131_TLR1 0.0029430826+-37TLR1 X131 4.639811up_regulated 2637959NA
10chr44083131640831336chr44002023940021517X15_KRT18P25 0.0377022971++20KRT18P25 X15 10.232980up_regulated 811077NA
11chr44163484541634865chr44389896143899351X151_NDUFB4P12 -0.5735367217++26NDUFB4P12 X151 9.274555down_regulated2264116NA
12chr44166078441660804chr44002023940021517X155_KRT18P25 0.1515830106++20KRT18P25 X155 15.869232up_regulated 1640545NA
13chr44170033941700359chr44174408141748725X170_PHOX2B 1.2739117586+-30PHOX2B X170 3.012733up_regulated 48386NA
15chr44175403741754057chr44187274641882955X173_LINC00682 0.4788132176+-23LINC00682 X173 3.273311up_regulated 128918NA
16chr44178252441782544chr43918250339285810X185_WDR19 -0.0084651451++43WDR19 X185 3.361500down_regulated2600021NA
17chr44178252441782544chr44033533240355217X185_CHRNA9 0.0025399652++14CHRNA9 X185 3.361500up_regulated 1447192NA
18chr44178252441782544chr43886767638945739X185_FAM114A1 0.1176303795++16FAM114A1 X185 3.017556up_regulated 2914848NA
20chr44180713041807150chr43879067638856817X199_TLR1 0.0021884797+-37TLR1 X199 6.224071up_regulated 2950313NA
21chr44180979741809817chr43997344339974338X200_PABPC1P1 0.0017952477++28PABPC1P1 X200 4.095850up_regulated 1836354NA
22chr44083601540836035chr44211085242152878X21_BEND4 0.0118460488+-13BEND4 X21 3.104921up_regulated 1316863NA
23chr44183879741838817chr44187274641882955X214_LINC00682 0.4489546782+-23LINC00682 X214 4.285326up_regulated 44158NA
24chr44183879741838817chr44174408141748725X214_PHOX2B 1.1657366751+-30PHOX2B X214 3.149307up_regulated 90072NA
25chr44188789141887911chr44174408141748725X228_PHOX2B 1.4376525900+-30PHOX2B X228 3.610373up_regulated 139166NA
26chr44204008042040100chr43879067638856817X244_TLR1 0.0041366603+-37TLR1 X244 4.365186up_regulated 3183263NA
27chr44214782242147842chr44033533240355217X254_CHRNA9 0.0043198282++14CHRNA9 X254 12.125825up_regulated 1812490NA
28chr44214914442149164chr44211085242152878X257_BEND4 0.2175680256+-13BEND4 X257 20.797436up_regulated 3734NA
29chr44214949442149514chr44211085242152878X260_BEND4 0.1327666209+-13BEND4 X260 16.773563up_regulated 3384NA
30chr44216547442165494chr44211085242152878X264_BEND4 0.0135461527+-13BEND4 X264 10.742606up_regulated 12596NA
31chr44218450142184521chr44031648440330419X265_LINC02265 0.0045985942++24LINC02265 X265 5.301508up_regulated 1868017NA
32chr44218458942184609chr44239748742402487X266_SHISA3 0.0753909420++34SHISA3 X266 3.082512up_regulated 212898NA
......................................................
188chr44230700342307023chr44239748742402487X898_SHISA3 -2.881370e-03++34SHISA3 X898 3.685833down_regulated 90484NA
189chr44230702942307049chr44239748742402487X899_SHISA3 3.661259e-01++34SHISA3 X899 26.044537up_regulated 90458NA
190chr44114400741144027chr44031648440330419X90_LINC02265 2.961355e-03++24LINC02265 X90 4.466547up_regulated 827523NA
191chr44239744742397467chr44239748742402487X910_SHISA3 4.664096e-01++34SHISA3 X910 4.527663up_regulated 40SHISA3
192chr44239751542397535chr44239748742402487X912_SHISA3 9.427664e-01++34SHISA3 X912 63.549336up_regulated 28SHISA3
193chr44239761142397631chr44239748742402487X913_SHISA3 9.012685e-01++34SHISA3 X913 16.047242up_regulated 124SHISA3
194chr44239764142397661chr44239748742402487X914_SHISA3 1.370495e+00++34SHISA3 X914 83.873479up_regulated 154SHISA3
195chr44239767942397699chr44239748742402487X915_SHISA3 6.755128e-01++34SHISA3 X915 55.427103up_regulated 192SHISA3
196chr44239843142398451chr44239748742402487X916_SHISA3 3.474206e-01++34SHISA3 X916 3.537265up_regulated 944NA
197chr44239857642398596chr44239748742402487X917_SHISA3 6.508450e-01++34SHISA3 X917 20.083096up_regulated 1089NA
198chr44248160342481623chr44239748742402487X926_SHISA3 2.747485e-01++34SHISA3 X926 5.276413up_regulated 84116NA
199chr44248161942481639chr44239748742402487X927_SHISA3 1.860490e-01++34SHISA3 X927 6.767309up_regulated 84132NA
200chr44248171642481736chr44031648440330419X929_LINC02265 1.504744e-03++24LINC02265 X929 3.340200up_regulated 2165232NA
201chr44248869142488711chr44389896143899351X931_NDUFB4P12 3.842238e-01++26NDUFB4P12 X931 3.483382up_regulated 1410270NA
202chr44249003942490059chr44074992440811184X936_NSUN7 7.410074e-04++27NSUN7 X936 4.030951up_regulated 1740115NA
203chr44249003942490059chr43963910639666879X936_AC108471.2 6.022433e-03++ 8AC108471.2X936 3.087727up_regulated 2850933NA
204chr44251391442513934chr43997344339974338X940_PABPC1P1 1.152369e-03++28PABPC1P1 X940 4.883506up_regulated 2540471NA
205chr44251397342513993chr44042326640630875X942_RBM47 3.030300e-03+-31RBM47 X942 10.036695up_regulated 1883098NA
206chr44251397342513993chr44239748742402487X942_SHISA3 3.267667e-01++34SHISA3 X942 4.352914up_regulated 116486NA
207chr44271824142718261chr44175034441757341X947_AC105389.1 7.327823e-04++ 6AC105389.1X947 4.743006up_regulated 967897NA
208chr44075589240755912chr44074992440811184X951_NSUN7 8.591669e-04++27NSUN7 X951 4.047217up_regulated 5968NA
209chr44075597940755999chr43879067638856817X952_TLR1 4.623949e-03+-37TLR1 X952 5.924312up_regulated 1899162NA
210chr44080252440802544chr44002023940021517X955_KRT18P25 1.048582e-01++20KRT18P25 X955 14.645500up_regulated 782285NA
211chr44239669142396711chr44239748742402487X971_SHISA3 2.104751e-01++34SHISA3 X971 4.643779up_regulated 796NA
212chr44082380440823824chr44005684940158252X977_N4BP2 1.813326e-01++25N4BP2 X977 3.940885up_regulated 766955NA
214chr44111027041110290chr43879067638856817X980_TLR1 -9.388096e-05+-37TLR1 X980 3.311899down_regulated2253453NA
215chr44132280741322827chr44468219944726588X984_GNPDA2 7.046911e-03+-17GNPDA2 X984 3.746113up_regulated 3403781NA
216chr44124628841246308chr44033533240355217X99_CHRNA9 4.876782e-03++14CHRNA9 X99 10.941710up_regulated 910956NA
217chr44109001641090036chr44468219944726588X997_GNPDA2 1.096161e-01+-17GNPDA2 X997 4.416889up_regulated 3636572NA
218chr44223967142239691chr44239748742402487X1030_SHISA3 1.093835e-01++34SHISA3 X1030 6.074699up_regulated 157816NA
In [125]:
genes.bed.detected <- genes.bed[genes.bed$gene %in% unique(TAP_DE$gene),]
In [126]:
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
In [127]:
table(jumped_gene_counts)
jumped_gene_counts
 0  1  2  3  4  5  6  7  8  9 10 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
58 23 12  7  4  4  2  5  4  8  5  3  4  5  4  3  3  4  6  3  3  2  6  7  4  2 
27 28 29 30 31 32 33 34 36 39 40 42 
 4  3  3  2  1  1  1  1  1  1  1  1 
In [128]:
## Skipped genes
length(jumped_gene_counts)-58
153
In [293]:
options(repr.plot.width=8, repr.plot.height=8)
boxplot(jumped_gene_counts, main="number of jumped genes", cex.lab=1.5)
summary(jumped_gene_counts)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   5.000   9.758  18.500  42.000 
In [294]:
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [295]:
pdf("Genes_jumped_202212.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2
In [296]:
barplot(table(jumped_gene_counts), xlab="Genes jumped", ylab="Counts", cex.lab=1.5, border = NA)
In [297]:
ghits.bedpe$jumped_gene_counts <- jumped_gene_counts
In [298]:
sig <- c()
count <- 0
sig_ratio <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
            sig <- c(sig, if(as.numeric(TAP_DE$p_val_adj[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])<0.01){"sig"}else{"non_sig"})
        }
        if(j == nrow(genes.bed.detected)){
            sig_ratio <- c(sig_ratio, if(count==0){1}else{length(which(sig=="sig"))/length(sig)})
            sig <- c()
            count <- 0
        }
   }
}
In [299]:
length(sig_ratio)
211
In [300]:
ghits.bedpe$sig_ratio <- sig_ratio
In [301]:
options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(aes(colour = sig_ratio),size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [302]:
options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [303]:
pdf("Genes_jumped_vs_pvalue_202212.pdf",width=6,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2

LFC target vs jumped¶

In [304]:
head(TAP_DE)
A data.frame: 6 × 10
p_valavg_logFCpct.1pct.2p_val_adjgeneidentmethodncellssignificance
<dbl><dbl><lgl><lgl><dbl><chr><chr><chr><int><chr>
10.04199363-0.015279653NANA0.9916263GNPDA2 X1MAST.cov22>=0.05
20.04758570 0.133542942NANA0.9916263RPS7P7 X1MAST.cov22>=0.05
30.09462442 0.001029732NANA0.9916263CHRNA9 X1MAST.cov22>=0.05
40.10635680 0.012400904NANA0.9916263KLHL5 X1MAST.cov22>=0.05
50.11720622 NANANA0.9916263AC095057.3X1MAST.cov22>=0.05
60.12308059-0.001536993NANA0.9916263PHOX2B X1MAST.cov22>=0.05
In [305]:
head(genes.bed.detected)
A data.frame: 6 × 7
chromstartstopgenescorestrandtype
<chr><dbl><dbl><chr><chr><chr><chr>
13chr43877223738782990TLR10 .-gene
14chr43879067638856817TLR1 .-gene
15chr43882371438856817TLR6 .-gene
16chr43886767638945739FAM114A1.+gene
18chr43896674339032922TMEM156 .-gene
19chr43904503839126857KLHL5 .+gene
In [306]:
jumped_gene_counts <- c()
LFC <- c()
LFC_diff <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            LFC <- c(LFC, if(!is.na(as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])]))){as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])})
        }
        if(j == nrow(genes.bed.detected)){
            LFC_diff <- c(LFC_diff, sum(ghits.bedpe$score[i]-LFC)/length(LFC))
            LFC <- c()
        }
   }
}
In [307]:
length(LFC_diff)
211
In [308]:
sum(is.na(LFC_diff))
67
In [309]:
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 67 rows containing non-finite values (`stat_bin()`).”
In [310]:
pdf("LFC_target_vs_jumped_202212.pdf",width=6,height=6)
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 67 rows containing non-finite values (`stat_bin()`).”
png: 2
In [311]:
hist(LFC_diff, main = "", xlab="LFC target genes vs. jumped genes", ylab="Counts", cex.lab=1.5, breaks=30)
In [312]:
ghits.bedpe$LFC_diff <- LFC_diff
In [313]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(LFC_diff, log_pvaladj))+ geom_point(size=4)+ theme_minimal() + xlab("LFC target genes vs. jumped genes") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
Warning message:
“Removed 67 rows containing missing values (`geom_point()`).”
In [314]:
summary(ghits.bedpe$LFC_diff)
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max.     NA's 
-1.02476 -0.04538  0.00420  0.06123  0.08660  1.36165       67 
In [315]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj)) +geom_point(size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [316]:
options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
`geom_smooth()` using formula = 'y ~ x'
In [317]:
options(repr.plot.width=12, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal()+ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,),axis.text.x = element_text(angle=60, hjust=1)
)
In [318]:
sort(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1], decreasing = TRUE)
X770 X808 X185 X512  X58 X829 X886 X124 X214 X283 X341 X350 X356 X380 X404 X572 
   5    5    3    3    3    3    3    2    2    2    2    2    2    2    2    2 
X624 X634 X651 X698 X717  X74 X780 X854 X882 X893 X936 X942 
   2    2    2    2    2    2    2    2    2    2    2    2 
In [319]:
names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1])
  1. 'X124'
  2. 'X185'
  3. 'X214'
  4. 'X283'
  5. 'X341'
  6. 'X350'
  7. 'X356'
  8. 'X380'
  9. 'X404'
  10. 'X512'
  11. 'X572'
  12. 'X58'
  13. 'X624'
  14. 'X634'
  15. 'X651'
  16. 'X698'
  17. 'X717'
  18. 'X74'
  19. 'X770'
  20. 'X780'
  21. 'X808'
  22. 'X829'
  23. 'X854'
  24. 'X882'
  25. 'X886'
  26. 'X893'
  27. 'X936'
  28. 'X942'
In [320]:
ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))
In [321]:
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()%>% arrange(gene)
In [322]:
nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000
In [323]:
#Type
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
In [324]:
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})
In [325]:
options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")
`geom_smooth()` using formula = 'y ~ x'
In [326]:
options(repr.plot.width=12, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal()+ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,),axis.text.x = element_text(angle=60, hjust=1)
)
In [327]:
ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))
In [328]:
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
gRNA.up.bed$gene <- gsub("PHOX2B.","B",gRNA.up.bed$gene)
In [329]:
nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000
In [330]:
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

From here region¶

In [209]:
ghits <- TAP_DE[grep("^Region", TAP_DE$ident),]
In [210]:
chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Region_name)]
start1 <- br_anno$Region_start[match(ghits$ident, br_anno$Region_name)]
end1 <- br_anno$Region_end[match(ghits$ident, br_anno$Region_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
ghits$ident <- gsub("^Region_","R",ghits$ident)
name <- paste0(ghits$ident,"_",ghits$gene)
ghits$ident <- gsub("^R","Region_",ghits$ident)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Region_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#avg_logFC <- ghits$avg_logFC
br_anno$Region_name <- gsub("^Region_","R",br_anno$Region_name)
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$Region_start, stop=br_anno$Region_end, gene=br_anno$Region_name, score=".", strand=br_anno$strand, type="gene")
gRNA.bed <- gRNA.bed[!is.na(gRNA.bed$gene),]
gRNA.bed <- gRNA.bed %>% distinct()
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
br_anno$Region_name <- gsub("^R","Region_",br_anno$Region_name)
In [211]:
## For region
#ghits.bedpe <- TAP_DE.bedpe[grep("^Region", TAP_DE.bedpe$gRNA),]
#ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$chrom1),]

#My definition of linear distance
#ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

##Scott's linear distance, always started from start site
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){abs(as.numeric(x[2])-as.numeric(x[5]))})
ghits.bedpe$significance <- rep("adj.pval >= 0.05", nrow(ghits.bedpe))
ghits.bedpe$significance[ghits.bedpe$log_pvaladj>1.3] <- "adj.pval < 0.05"

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS/1000000, log_pvaladj)) +geom_point(aes(colour = significance),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="Region")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [212]:
ghits.bedpe <- ghits.bedpe %>% filter(significance=="adj.pval < 0.05")
In [213]:
summary(ghits.bedpe$distance.TSS)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
     97  195534 1258251 1356463 2265607 3942865 
In [231]:
pdf("Distance_to_TSS_vs_pvalue_region_202212.pdf",width=8,height=6)
ggplot(ghits.bedpe, aes(distance.TSS/1000000, log_pvaladj)) +geom_point(aes(colour = significance),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="Region")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [214]:
ghits <- rhits
In [215]:
colnames(br_anno)
  1. 'Region_name'
  2. 'Region_pvalue'
  3. 'Region_fdr'
  4. 'Region_slope'
  5. 'Chr'
  6. 'Region_start'
  7. 'Region_end'
  8. 'Bins_in_region'
  9. 'Bin'
  10. 'Bin_slope'
  11. 'Bin_pvalue'
  12. 'Bin_fdr'
  13. 'Bin_speed'
  14. 'Bin_start'
  15. 'Bin_end'
  16. 'guide_start'
  17. 'guide_end'
  18. 'strand'
  19. 'guide_sequence'
  20. 'guide_replicate'
  21. 'guide_name'
  22. 'guide_logfold'
  23. 'guide_pvalue'
  24. 'giude_classification'
  25. 'guide_fdr'
  26. 'Rhapsody_name'
  27. 'class'
In [216]:
chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Region_name)]
start1 <- br_anno$Region_start[match(ghits$ident, br_anno$Region_name)]
end1 <- br_anno$Region_end[match(ghits$ident, br_anno$Region_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
ghits$ident <- gsub("^Region_","R",ghits$ident)
name <- paste0(ghits$ident,"_",ghits$gene)
ghits$ident <- gsub("^R","Region_",ghits$ident)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Region_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
br_anno$Region_name <- gsub("^Region_","R",br_anno$Region_name)
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$Region_start, stop=br_anno$Region_end, gene=br_anno$Region_name, score=".", strand=br_anno$strand, type="gene")
gRNA.bed <- gRNA.bed[!is.na(gRNA.bed$gene),]
gRNA.bed <- gRNA.bed %>% distinct()
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
br_anno$Region_name <- gsub("^R","Region_",br_anno$Region_name)
In [217]:
head(ghits.bedpe)
A data.frame: 6 x 15
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtype
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr>
1chr44074931540752221chr44042326640630875R1_RBM47 0.0001855366+-22RBM47 Region_1 4.697194up_regulated
2chr44074931540752221chr44074992440811184R1_NSUN7 0.0049871483++18NSUN7 Region_1 3.452971up_regulated
3chr44074931540752221chr44247180942472380R1_RPS7P7 0.1037766838++23RPS7P7 Region_1 3.452971up_regulated
4chr44101267141016125chr44002023940021517R132_KRT18P25 0.0243873463++13KRT18P25 Region_13212.467571up_regulated
5chr44101267141016125chr44469394544694386R132_AC096586.2-0.0003783229+- 3AC096586.2Region_132 3.386169down_regulated
6chr44105031141051029chr44389896143899351R152_NDUFB4P12 0.2486232951++17NDUFB4P12 Region_152 4.827161up_regulated
In [201]:
#meta <- read.table("../../CW_data/Dusa/lastForCheWei.tsv", sep="\t", head=TRUE)
#meta$ident <- gsub("egion_","",meta$ident)
#meta <- meta %>% mutate(name = paste0(ident,"_",gene))
#ghits.bedpe <- left_join(ghits.bedpe, meta, by = "name")
#ghits.bedpe[is.na(ghits.bedpe)] <- 0
In [202]:
#head(ghits.bedpe)
A data.frame: 6 x 53
chrom1start1end1chrom2start2end2namescorestrand1strand2...maxAbcScoreregionH3K27acgeneH3K27acregionH3K4me1geneH3K4me1regionAtacgeneAtacregionH3K4me3geneH3K4me3gc
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr>...<dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl>
1chr44074931540752221chr44042326640630875R1_RBM47 0.0001855366+-...0.055817125.748503 3.99201643.912176 5.988024238.52295 50.89820254.491018 3.9920160.523400
2chr44074931540752221chr44074992440811184R1_NSUN7 0.0049871483++...0.293307125.748503249.50099843.91217624.950100238.52295434.13174254.491018392.2155690.523400
3chr44074931540752221chr44247180942472380R1_RPS7P7 0.1037766838++...0.000000125.748503 1.99600843.912176 2.994012238.52295 21.95609254.491018 2.9940120.523400
4chr44101267141016125chr44002023940021517R132_KRT18P25 0.0243873463++...0.000000 0.000000 0.000000 1.996008 0.000000 22.95409 18.96208 0.000000 3.9920160.403301
5chr44101267141016125chr44469394544694386R132_AC096586.2-0.0003783229+-...0.000000 0.000000 0.000000 1.996008 2.994012 22.95409 32.93413 0.000000 4.9900200.403301
6chr44105031141051029chr44389896143899351R152_NDUFB4P12 0.2486232951++...0.000000 1.996008 8.982036 6.986028 2.994012 29.94012 10.97804 3.992016 1.9960080.452646
In [164]:
colnames(ghits.bedpe)
  1. 'chrom1'
  2. 'start1'
  3. 'end1'
  4. 'chrom2'
  5. 'start2'
  6. 'end2'
  7. 'name'
  8. 'score'
  9. 'strand1'
  10. 'strand2'
  11. 'samplenumber'
  12. 'gene.x'
  13. 'gRNA'
  14. 'log_pvaladj'
  15. 'type'
  16. 'p_val'
  17. 'avg_logFC'
  18. 'pct.1'
  19. 'pct.2'
  20. 'p_val_adj'
  21. 'gene.y'
  22. 'ident'
  23. 'method'
  24. 'ncells'
  25. 'pairId'
  26. 'regionChr'
  27. 'regionStart'
  28. 'regionEnd'
  29. 'geneTssChr'
  30. 'geneTssStart'
  31. 'geneTssEnd'
  32. 'width'
  33. 'class'
  34. 'tissue'
  35. 'bulkPromHit'
  36. 'sig'
  37. 'dist'
  38. 'hicScore'
  39. 'hicInteracts'
  40. 'maxCapcScore'
  41. 'capcInteracts'
  42. 'interacts'
  43. 'maxEpiMapLinkScore'
  44. 'maxAbcScore'
  45. 'regionH3K27ac'
  46. 'geneH3K27ac'
  47. 'regionH3K4me1'
  48. 'geneH3K4me1'
  49. 'regionAtac'
  50. 'geneAtac'
  51. 'regionH3K4me3'
  52. 'geneH3K4me3'
  53. 'gc'
In [165]:
ghits.bedpe$gene.x
  1. 'RBM47'
  2. 'NSUN7'
  3. 'RPS7P7'
  4. 'KRT18P25'
  5. 'AC096586.2'
  6. 'NDUFB4P12'
  7. 'NDUFB4P12'
  8. 'APBB2'
  9. 'TLR1'
  10. 'LINC02265'
  11. 'KRT18P25'
  12. 'APBB2'
  13. 'CHRNA9'
  14. 'PDS5A'
  15. 'TLR1'
  16. 'N4BP2'
  17. 'LINC00682'
  18. 'KRT18P25'
  19. 'GNPDA2'
  20. 'RPS7P7'
  21. 'PHOX2B'
  22. 'PHOX2B'
  23. 'SLC30A9'
  24. 'ARL4AP2'
  25. 'PHOX2B'
  26. 'PHOX2B'
  27. 'APBB2'
  28. 'PHOX2B'
  29. 'PABPC1P1'
  30. 'PHOX2B'
  31. 'LINC00682'
  32. 'PHOX2B'
  33. 'LINC00682'
  34. 'PHOX2B'
  35. 'LINC00682'
  36. 'PHOX2B'
  37. 'PHOX2B'
  38. 'PHOX2B'
  39. 'LINC00682'
  40. 'PHOX2B'
  41. 'RPS7P7'
  42. 'AC095057.3'
  43. 'SLC30A9'
  44. 'TLR1'
  45. 'AC096586.1'
  46. 'TMEM33'
  47. 'AC105389.1'
  48. 'LINC02265'
  49. 'CHRNA9'
  50. 'CHRNA9'
  51. 'BEND4'
  52. 'BEND4'
  53. 'AC098590.1'
  54. 'CHRNA9'
  55. 'NSUN7'
  56. 'LINC02265'
  57. 'SHISA3'
  58. 'ZBTB12BP'
  59. 'BEND4'
  60. 'SHISA3'
  61. 'SHISA3'
  62. 'SHISA3'
  63. 'BEND4'
  64. 'SHISA3'
  65. 'RPS7P7'
  66. 'SHISA3'
  67. 'SHISA3'
  68. 'SHISA3'
  69. 'TLR6'
  70. 'UGDH'
  71. 'SHISA3'
  72. 'SHISA3'
  73. 'TMEM156'
  74. 'PABPC1P1'
  75. 'SHISA3'
  76. 'ARL4AP2'
  77. 'RPS7P7'
  78. 'ATP8A1'
  79. 'SHISA3'
  80. 'TLR6'
  81. 'LINC02265'
  82. 'SHISA3'
  83. 'SHISA3'
  84. 'ATP8A1'
  85. 'SHISA3'
  86. 'AC096734.2'
  87. 'ATP8A1'
  88. 'WDR19'
  89. 'GNPDA2'
  90. 'PHOX2B'
  91. 'TMEM156'
In [166]:
ghits.bedpe$gene.y
  1. 'RBM47'
  2. 'NSUN7'
  3. 'RPS7P7'
  4. 'KRT18P25'
  5. 'AC096586.2'
  6. 'NDUFB4P12'
  7. 'NDUFB4P12'
  8. 'APBB2'
  9. 'TLR1'
  10. 'LINC02265'
  11. 'KRT18P25'
  12. 'APBB2'
  13. 'CHRNA9'
  14. 'PDS5A'
  15. 'TLR1'
  16. 'N4BP2'
  17. 'LINC00682'
  18. 'KRT18P25'
  19. 'GNPDA2'
  20. 'RPS7P7'
  21. 'PHOX2B'
  22. 'PHOX2B'
  23. 'SLC30A9'
  24. 'ARL4AP2'
  25. 'PHOX2B'
  26. 'PHOX2B'
  27. 'APBB2'
  28. 'PHOX2B'
  29. 'PABPC1P1'
  30. 'PHOX2B'
  31. 'LINC00682'
  32. 'PHOX2B'
  33. 'LINC00682'
  34. 'PHOX2B'
  35. 'LINC00682'
  36. 'PHOX2B'
  37. 'PHOX2B'
  38. 'PHOX2B'
  39. 'LINC00682'
  40. 'PHOX2B'
  41. 'RPS7P7'
  42. 'AC095057.3'
  43. 'SLC30A9'
  44. 'TLR1'
  45. 'AC096586.1'
  46. 'TMEM33'
  47. 'AC105389.1'
  48. 'LINC02265'
  49. 'CHRNA9'
  50. 'CHRNA9'
  51. 'BEND4'
  52. 'BEND4'
  53. 'AC098590.1'
  54. 'CHRNA9'
  55. 'NSUN7'
  56. 'LINC02265'
  57. 'SHISA3'
  58. 'ZBTB12BP'
  59. 'BEND4'
  60. 'SHISA3'
  61. 'SHISA3'
  62. 'SHISA3'
  63. 'BEND4'
  64. 'SHISA3'
  65. 'RPS7P7'
  66. 'SHISA3'
  67. 'SHISA3'
  68. 'SHISA3'
  69. 'TLR6'
  70. 'UGDH'
  71. 'SHISA3'
  72. 'SHISA3'
  73. 'TMEM156'
  74. 'PABPC1P1'
  75. 'SHISA3'
  76. 'ARL4AP2'
  77. 'RPS7P7'
  78. 'ATP8A1'
  79. 'SHISA3'
  80. 'TLR6'
  81. 'LINC02265'
  82. 'SHISA3'
  83. 'SHISA3'
  84. 'ATP8A1'
  85. 'SHISA3'
  86. 'AC096734.2'
  87. 'ATP8A1'
  88. 'WDR19'
  89. 'GNPDA2'
  90. 'PHOX2B'
  91. 'TMEM156'
In [167]:
nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000
In [257]:
#Type
pdf("track_regulation_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
dev.off()

#Log_FoldChange
pdf("track_avg_logFC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()

#Hi-C
pdf("track_Hi-C_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$hicScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
dev.off()

#CaptureC
pdf("track_CaptureC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$maxCapcScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
dev.off()

#GeneTrack
pdf("track_gene_region_202212.pdf",width=16,height=1.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()

#gRNATRACK
pdf("track_region_region_202212.pdf",width=16,height=3)
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("region",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
png: 2
[1] "yes"
png: 2
In [256]:
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=4)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#Hi-C
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$hicScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
#CaptureC
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$maxCapcScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=3)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("region",side=2,line=3,cex=1,font=2)
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
In [168]:
ghits.bedpe.PHOX2B <- ghits.bedpe %>% filter(gene.x == "PHOX2B")
In [169]:
head(ghits.bedpe.PHOX2B)
A data.frame: 6 x 53
chrom1start1end1chrom2start2end2namescorestrand1strand2...maxAbcScoreregionH3K27acgeneH3K27acregionH3K4me1geneH3K4me1regionAtacgeneAtacregionH3K4me3geneH3K4me3gc
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr>...<dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl>
1chr44171363041714666chr44174408141748725R477_PHOX2B 0.4677258+-...0.000000 38.922156441.1178 24.95010011.97605 52.89421753.493 0.998004431.13770.383205
2chr44174871141752752chr44174408141748725R494_PHOX2B-0.5493911+-...0.206476639.720559441.1178 49.90020011.97605252.49501753.49378.842315431.13770.493195
3chr44177112941772268chr44174408141748725R504_PHOX2B 0.3603152+-...0.000000 0.998004441.1178 0.99800411.97605 35.92814753.493 2.994012431.13770.399473
4chr44178441741785468chr44174408141748725R512_PHOX2B-0.3404573+-...0.019211430.139721441.1178140.71856311.97605788.42315753.493 7.984032431.13770.426261
5chr44179589241798240chr44174408141748725R520_PHOX2B 0.4048890+-...0.085094114.770459441.1178145.70858311.97605105.78842753.493 4.990020431.13770.445486
6chr44181377841822745chr44174408141748725R530_PHOX2B-0.3854239+-...0.000000 20.958084441.1178 25.94810411.97605 55.88822753.493 0.998004431.13770.432140
In [170]:
chrom = "chr4"
chromstart = 41600000
chromend = 41900000
In [281]:
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$score,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#Hi-C
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$hicScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
#CaptureC
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$maxCapcScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"
In [282]:
pdf("PHOX2B_track_avg_logFC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$score,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_Hi-C_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$hicScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_CaptureC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$maxCapcScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_gene_region_202212.pdf",width=16,height=1.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
[1] "yes"
png: 2
[1] "yes"
png: 2
In [218]:
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})
In [148]:
options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")
`geom_smooth()` using formula = 'y ~ x'
In [344]:
options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")
`geom_smooth()` using formula = 'y ~ x'
In [149]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal() +ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=15),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))
In [345]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal() +ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=15),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))
In [219]:
ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))
In [220]:
ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
In [221]:
median(ghits.bedpe$distance.TSS)
485634
In [222]:
length(table(ghits.bedpe$gRNA))
21
In [223]:
genes.up.bed
A data.frame: 28 x 8
chromstartstopgenescorestrandtypeorder
<chr><dbl><dbl><chr><chr><chr><chr><int>
55chr44016667440167831AC095057.3.+gene 55
125chr44470440444704965AC096586.1.+gene125
124chr44469394544694386AC096586.2.-gene124
110chr44341004043410937AC098590.1.-gene110
85chr44175034441757341AC105389.1.+gene 85
68chr44078610940786710ARL4AP2 .+gene 68
100chr44240837242657105ATP8A1 .-gene100
96chr44211085242152878BEND4 .-gene 96
60chr44033533240355217CHRNA9 .+gene 60
123chr44468219944726588GNPDA2 .-gene123
49chr44002023940021517KRT18P25 .+gene 49
88chr44187274641882955LINC00682 .-gene 88
59chr44031648440330419LINC02265 .+gene 59
67chr44074992440811184NSUN7 .+gene 67
48chr43997344339974338PABPC1P1 .+gene 48
44chr43982286239977956PDS5A .-gene 44
83chr44174408141748725PHOX2B .-gene 83
62chr44042326640630875RBM47 .-gene 62
101chr44247180942472380RPS7P7 .+gene101
99chr44239748742402487SHISA3 .+gene 99
94chr44199050142090461SLC30A9 .+gene 94
14chr43879067638856817TLR1 .-gene 14
15chr43882371438856817TLR6 .-gene 15
18chr43896674339032922TMEM156 .-gene 18
91chr44193512841960803TMEM33 .+gene 91
32chr43949875439528311UGDH .-gene 32
22chr43918250339285810WDR19 .+gene 22
43chr43977008039771371ZBTB12BP .-gene 43
In [224]:
pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
ghits.bedpe %>% filter(promoter!="NA")
A data.frame: 3 x 17
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtypedistance.TSSpromoter
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr><dbl><chr>
chr44239737742398743chr44239748742402487R790_SHISA3 0.6905067398++20SHISA3Region_790191.839188up_regulated 110SHISA3
chr44239737742398743chr43882371438856817R790_TLR6 -0.0001907844+-23TLR6 Region_790 3.368763down_regulated3540560SHISA3
chr44239737742398743chr43949875439528311R790_UGDH -0.0018959126+-26UGDH Region_790 3.368763down_regulated2869066SHISA3
In [225]:
pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
ghits.bedpe %>% filter(promoter!="NA")
A data.frame: 3 x 17
chrom1start1end1chrom2start2end2namescorestrand1strand2samplenumbergenegRNAlog_pvaladjtypedistance.TSSpromoter
<chr><int><int><chr><dbl><dbl><chr><dbl><chr><chr><dbl><chr><chr><dbl><chr><dbl><chr>
chr44239737742398743chr44239748742402487R790_SHISA3 0.6905067398++20SHISA3Region_790191.839188up_regulated 110SHISA3
chr44239737742398743chr43882371438856817R790_TLR6 -0.0001907844+-23TLR6 Region_790 3.368763down_regulated3540560SHISA3
chr44239737742398743chr43949875439528311R790_UGDH -0.0018959126+-26UGDH Region_790 3.368763down_regulated2869066SHISA3

Jumpe genes (region)¶

In [226]:
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})
In [227]:
pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
In [235]:
length(unique(TAP_DE$gene))
59
In [238]:
unique(TAP_DE$gene)
  1. 'GNPDA2'
  2. 'RPS7P7'
  3. 'CHRNA9'
  4. 'KLHL5'
  5. 'AC095057.3'
  6. 'PHOX2B'
  7. 'AC096586.1'
  8. 'AC079921.2'
  9. 'BEND4'
  10. 'TLR1'
  11. 'WDR19'
  12. 'RBM47'
  13. 'GUF1'
  14. 'TMEM33'
  15. 'SMIM14'
  16. 'KRT18P25'
  17. 'FAM114A1'
  18. 'AC105389.1'
  19. 'ATP8A1'
  20. 'APBB2'
  21. 'TLR6'
  22. 'AC108471.2'
  23. 'AC106052.1'
  24. 'NSUN7'
  25. 'AC096586.2'
  26. 'NDUFB4P12'
  27. 'LINC02265'
  28. 'AC098591.1'
  29. 'AC098591.2'
  30. 'ARL4AP2'
  31. 'RFC1'
  32. 'DCAF4L1'
  33. 'N4BP2'
  34. 'AC096734.1'
  35. 'LINC00682'
  36. 'PDS5A'
  37. 'SLC30A9'
  38. 'TMEM156'
  39. 'LIAS'
  40. 'SHISA3'
  41. 'LIMCH1'
  42. 'PABPC1P1'
  43. 'AC021148.1'
  44. 'ATP1B1P1'
  45. 'UBE2K'
  46. 'ZBTB12BP'
  47. 'UCHL1.AS1'
  48. 'AC105389.3'
  49. 'UCHL1'
  50. 'AC096734.2'
  51. 'AC024022.1'
  52. 'RPL12P20'
  53. 'YIPF7'
  54. 'UGDH'
  55. 'AC098590.1'
  56. 'TLR10'
  57. 'LINC02475'
  58. 'AC108210.1'
  59. 'AC111006.1'

Only coding genes¶

In [267]:
ghits.bedpe.coding <- ghits.bedpe %>% filter( gene %in% coding_genes)
In [268]:
genes.bed.detected <- genes.bed[genes.bed$gene %in% coding_genes,] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe.coding)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe.coding$start1[i],ghits.bedpe.coding$start2[i],ghits.bedpe.coding$end1[i],ghits.bedpe.coding$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe.coding$start1[i],ghits.bedpe.coding$start2[i],ghits.bedpe.coding$end1[i],ghits.bedpe.coding$end2[i])) & ghits.bedpe.coding$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)
jumped_gene_counts
 0  2  3  8  9 10 12 14 15 20 21 22 23 
18  4  2  1  1  1  1  1  1  1  1  1  1 
In [269]:
## Skipped genes
length(jumped_gene_counts)-18
16
In [270]:
ghits.bedpe.coding$jumped_gene_counts <- jumped_gene_counts
In [271]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe.coding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of coding genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
In [272]:
pdf("Coding_genes_jumped_region_with_logFC_pval_202502.pdf",width=8,height=6)
ggplot(ghits.bedpe.coding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of coding genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()
png: 2
In [273]:
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Coding genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [274]:
pdf("Coding_genes_jumped_region_202502.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Coding genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2

Only Non-coding genes/ Pseudogenes considered¶

In [275]:
ghits.bedpe.ncoding <- ghits.bedpe %>% filter( gene %in% non_coding_genes)
In [276]:
genes.bed.detected <- genes.bed[genes.bed$gene %in% non_coding_genes,] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe.ncoding)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe.ncoding$start1[i],ghits.bedpe.ncoding$start2[i],ghits.bedpe.ncoding$end1[i],ghits.bedpe.ncoding$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe.ncoding$start1[i],ghits.bedpe.ncoding$start2[i],ghits.bedpe.ncoding$end1[i],ghits.bedpe.ncoding$end2[i])) & ghits.bedpe.ncoding$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)
jumped_gene_counts
 0  4  5  7  9 10 11 12 16 17 
 5  3  1  1  1  1  1  1  3  1 
In [277]:
## Skipped genes
length(jumped_gene_counts)-5
13
In [278]:
ghits.bedpe.ncoding$jumped_gene_counts <- jumped_gene_counts
In [279]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe.ncoding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of non-coding/pseudo genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
In [280]:
pdf("Non_coding_genes_jumped_region_with_logFC_pval_202502.pdf",width=8,height=6)
ggplot(ghits.bedpe.ncoding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of non-coding/pseudo genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()
png: 2
In [281]:
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Non-coding/pseudo genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [282]:
pdf("Non_coding_pseudo_genes_jumped_region_202502.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Non-coding/pseudo genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2

All genes considered¶

In [228]:
genes.bed.detected <- genes.bed[genes.bed$gene %in% unique(TAP_DE$gene),] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)
jumped_gene_counts
 0  1  2  3  4  6  7  9 14 17 18 19 21 23 24 26 28 29 34 42 43 45 
13  7  2  1  2  1  3  4  1  1  1  3  1  1  2  1  1  2  1  1  2  1 
In [229]:
## Skipped genes
length(jumped_gene_counts)-13
39
In [160]:
options(repr.plot.width=8, repr.plot.height=8)
boxplot(jumped_gene_counts, main="number of jumped genes", cex.lab=1.5)
summary(jumped_gene_counts)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.00    0.75    6.50   11.58   19.50   45.00 
In [230]:
ghits.bedpe$jumped_gene_counts <- jumped_gene_counts
In [231]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
In [176]:
pdf("Genes_jumped_region_with_logFC_pval_202407.pdf",width=8,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()
png: 2
In [232]:
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
In [358]:
pdf("Genes_jumped__region_202212.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
png: 2
In [359]:
ghits.bedpe$jumped_gene_counts <- jumped_gene_counts
sig <- c()
count <- 0
sig_ratio <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
            sig <- c(sig, if(as.numeric(TAP_DE$p_val_adj[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])<0.01){"sig"}else{"non_sig"})
        }
        if(j == nrow(genes.bed.detected)){
            sig_ratio <- c(sig_ratio, if(count==0){1}else{length(which(sig=="sig"))/length(sig)})
            sig <- c()
            count <- 0
        }
   }
}
ghits.bedpe$sig_ratio <- sig_ratio
In [360]:
options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(aes(colour = sig_ratio),size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [361]:
options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
In [362]:
pdf("Genes_jumped_vs_pvalue_region_202212.pdf",width=6,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()
png: 2
In [363]:
jumped_gene_counts <- c()
LFC <- c()
LFC_diff <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            LFC <- c(LFC, if(!is.na(as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])]))){as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])})
        }
        if(j == nrow(genes.bed.detected)){
            LFC_diff <- c(LFC_diff, sum(ghits.bedpe$score[i]-LFC)/length(LFC))
            LFC <- c()
        }
   }
}

length(LFC_diff)
sum(is.na(LFC_diff))
52
16
In [364]:
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 16 rows containing non-finite values (`stat_bin()`).”
In [365]:
pdf("LFC_target_vs_jumped_region_202212.pdf",width=6,height=6)
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 16 rows containing non-finite values (`stat_bin()`).”
png: 2
In [366]:
hist(LFC_diff, main = "", xlab="LFC target genes vs. jumped genes", ylab="Counts", cex.lab=1.5, breaks=30)
In [367]:
ghits.bedpe$LFC_diff <- LFC_diff
In [368]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(LFC_diff, log_pvaladj))+ geom_point(size=4)+ theme_minimal() + xlab("LFC target genes vs. jumped genes") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
Warning message:
“Removed 16 rows containing missing values (`geom_point()`).”
In [369]:
options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj)) +geom_point(size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
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